Matching samples

GSE50760 · Gene expression profiling study by RNA-seq in colorectal cancer

Download matching samples CSV
Selected cohort requirements

Samples meeting selected requirements: 0 cases / 0 controls

36 case / 18 control samples elsewhere in the study have incomplete or conflicting evidence; they are not included above

Patient pairs verified in indexed sample metadata: 0

A case/control comparison meeting these requirements is not confirmed.

Counts describe samples, not independent patients. Pair verification uses explicit subject identifiers in indexed sample metadata. Zero verified pairs does not establish that the study is unpaired; reported matched-normal design alone is insufficient.

The CSV contains only the confirmed cases and controls below. Excluded and uncertain samples are shown for review and are not exported.

These are sample eligibility decisions from the current indexed metadata. Study-level search filters and minimum sample counts do not establish expression quality or analysis readiness.

Included samples (0)

No samples meet the selected requirements. The CSV contains its column headers only.

Uncertain samples (54)

These samples need more evidence before they can be counted. This includes samples without a confirmed case/control role.

GSM1228184

Uncertain

primary colorectal cancer AMC_2-1

Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Case marker detected.

Requirements and decision evidence
  • organism: Homo sapiens — Meets requirement
    • Supported by the indexed evidence.
    • organism_evidence_text: Homo sapiens
  • assay type: bulk RNA-seq — Meets requirement
    • Supported by the indexed evidence.
    • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
  • specimen category: Tissue or biopsy — Insufficient evidence
    • The required value is not reported.
    • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
      • Supported by the indexed evidence.
      • specimen category excludes: Biofluid — Meets requirement
        • Supported by the indexed evidence.
        Source metadata
        Source name
        primary colorectal cancer
        Characteristics
        tissue: primary colorectal cancer; ajcc stage: Stage IV
        Description
        Not reported
        Indexed organism evidence
        REPORTED · SAMPLE_REPORTED: Homo sapiens
        Indexed assay evidence
        MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
        Source
        GEO
        Original indexed metadata
        sample_accession: GSM1228184
sample_title: primary colorectal cancer AMC_2-1
source_name: primary colorectal cancer
characteristics: tissue: primary colorectal cancer; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

        GSM1228185

        Uncertain

        primary colorectal cancer AMC_3-1

        Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Case marker detected.

        Requirements and decision evidence
        • organism: Homo sapiens — Meets requirement
          • Supported by the indexed evidence.
          • organism_evidence_text: Homo sapiens
        • assay type: bulk RNA-seq — Meets requirement
          • Supported by the indexed evidence.
          • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
        • specimen category: Tissue or biopsy — Insufficient evidence
          • The required value is not reported.
          • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
            • Supported by the indexed evidence.
            • specimen category excludes: Biofluid — Meets requirement
              • Supported by the indexed evidence.
              Source metadata
              Source name
              primary colorectal cancer
              Characteristics
              tissue: primary colorectal cancer; ajcc stage: Stage IV
              Description
              Not reported
              Indexed organism evidence
              REPORTED · SAMPLE_REPORTED: Homo sapiens
              Indexed assay evidence
              MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
              Source
              GEO
              Original indexed metadata
              sample_accession: GSM1228185
sample_title: primary colorectal cancer AMC_3-1
source_name: primary colorectal cancer
characteristics: tissue: primary colorectal cancer; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

              GSM1228186

              Uncertain

              primary colorectal cancer AMC_5-1

              Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Case marker detected.

              Requirements and decision evidence
              • organism: Homo sapiens — Meets requirement
                • Supported by the indexed evidence.
                • organism_evidence_text: Homo sapiens
              • assay type: bulk RNA-seq — Meets requirement
                • Supported by the indexed evidence.
                • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
              • specimen category: Tissue or biopsy — Insufficient evidence
                • The required value is not reported.
                • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                  • Supported by the indexed evidence.
                  • specimen category excludes: Biofluid — Meets requirement
                    • Supported by the indexed evidence.
                    Source metadata
                    Source name
                    primary colorectal cancer
                    Characteristics
                    tissue: primary colorectal cancer; ajcc stage: Stage IV
                    Description
                    Not reported
                    Indexed organism evidence
                    REPORTED · SAMPLE_REPORTED: Homo sapiens
                    Indexed assay evidence
                    MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                    Source
                    GEO
                    Original indexed metadata
                    sample_accession: GSM1228186
sample_title: primary colorectal cancer AMC_5-1
source_name: primary colorectal cancer
characteristics: tissue: primary colorectal cancer; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                    GSM1228187

                    Uncertain

                    primary colorectal cancer AMC_6-1

                    Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Case marker detected.

                    Requirements and decision evidence
                    • organism: Homo sapiens — Meets requirement
                      • Supported by the indexed evidence.
                      • organism_evidence_text: Homo sapiens
                    • assay type: bulk RNA-seq — Meets requirement
                      • Supported by the indexed evidence.
                      • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                    • specimen category: Tissue or biopsy — Insufficient evidence
                      • The required value is not reported.
                      • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                        • Supported by the indexed evidence.
                        • specimen category excludes: Biofluid — Meets requirement
                          • Supported by the indexed evidence.
                          Source metadata
                          Source name
                          primary colorectal cancer
                          Characteristics
                          tissue: primary colorectal cancer; ajcc stage: Stage IV
                          Description
                          Not reported
                          Indexed organism evidence
                          REPORTED · SAMPLE_REPORTED: Homo sapiens
                          Indexed assay evidence
                          MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                          Source
                          GEO
                          Original indexed metadata
                          sample_accession: GSM1228187
sample_title: primary colorectal cancer AMC_6-1
source_name: primary colorectal cancer
characteristics: tissue: primary colorectal cancer; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                          GSM1228188

                          Uncertain

                          primary colorectal cancer AMC_7-1

                          Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Case marker detected.

                          Requirements and decision evidence
                          • organism: Homo sapiens — Meets requirement
                            • Supported by the indexed evidence.
                            • organism_evidence_text: Homo sapiens
                          • assay type: bulk RNA-seq — Meets requirement
                            • Supported by the indexed evidence.
                            • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                          • specimen category: Tissue or biopsy — Insufficient evidence
                            • The required value is not reported.
                            • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                              • Supported by the indexed evidence.
                              • specimen category excludes: Biofluid — Meets requirement
                                • Supported by the indexed evidence.
                                Source metadata
                                Source name
                                primary colorectal cancer
                                Characteristics
                                tissue: primary colorectal cancer; ajcc stage: Stage IV
                                Description
                                Not reported
                                Indexed organism evidence
                                REPORTED · SAMPLE_REPORTED: Homo sapiens
                                Indexed assay evidence
                                MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                                Source
                                GEO
                                Original indexed metadata
                                sample_accession: GSM1228188
sample_title: primary colorectal cancer AMC_7-1
source_name: primary colorectal cancer
characteristics: tissue: primary colorectal cancer; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                                GSM1228189

                                Uncertain

                                primary colorectal cancer AMC_8-1

                                Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Case marker detected.

                                Requirements and decision evidence
                                • organism: Homo sapiens — Meets requirement
                                  • Supported by the indexed evidence.
                                  • organism_evidence_text: Homo sapiens
                                • assay type: bulk RNA-seq — Meets requirement
                                  • Supported by the indexed evidence.
                                  • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                                • specimen category: Tissue or biopsy — Insufficient evidence
                                  • The required value is not reported.
                                  • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                                    • Supported by the indexed evidence.
                                    • specimen category excludes: Biofluid — Meets requirement
                                      • Supported by the indexed evidence.
                                      Source metadata
                                      Source name
                                      primary colorectal cancer
                                      Characteristics
                                      tissue: primary colorectal cancer; ajcc stage: Stage IV
                                      Description
                                      Not reported
                                      Indexed organism evidence
                                      REPORTED · SAMPLE_REPORTED: Homo sapiens
                                      Indexed assay evidence
                                      MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                                      Source
                                      GEO
                                      Original indexed metadata
                                      sample_accession: GSM1228189
sample_title: primary colorectal cancer AMC_8-1
source_name: primary colorectal cancer
characteristics: tissue: primary colorectal cancer; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                                      GSM1228190

                                      Uncertain

                                      primary colorectal cancer AMC_9-1

                                      Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Case marker detected.

                                      Requirements and decision evidence
                                      • organism: Homo sapiens — Meets requirement
                                        • Supported by the indexed evidence.
                                        • organism_evidence_text: Homo sapiens
                                      • assay type: bulk RNA-seq — Meets requirement
                                        • Supported by the indexed evidence.
                                        • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                                      • specimen category: Tissue or biopsy — Insufficient evidence
                                        • The required value is not reported.
                                        • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                                          • Supported by the indexed evidence.
                                          • specimen category excludes: Biofluid — Meets requirement
                                            • Supported by the indexed evidence.
                                            Source metadata
                                            Source name
                                            primary colorectal cancer
                                            Characteristics
                                            tissue: primary colorectal cancer; ajcc stage: Stage IV
                                            Description
                                            Not reported
                                            Indexed organism evidence
                                            REPORTED · SAMPLE_REPORTED: Homo sapiens
                                            Indexed assay evidence
                                            MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                                            Source
                                            GEO
                                            Original indexed metadata
                                            sample_accession: GSM1228190
sample_title: primary colorectal cancer AMC_9-1
source_name: primary colorectal cancer
characteristics: tissue: primary colorectal cancer; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                                            GSM1228191

                                            Uncertain

                                            primary colorectal cancer AMC_10-1

                                            Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Case marker detected.

                                            Requirements and decision evidence
                                            • organism: Homo sapiens — Meets requirement
                                              • Supported by the indexed evidence.
                                              • organism_evidence_text: Homo sapiens
                                            • assay type: bulk RNA-seq — Meets requirement
                                              • Supported by the indexed evidence.
                                              • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                                            • specimen category: Tissue or biopsy — Insufficient evidence
                                              • The required value is not reported.
                                              • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                                                • Supported by the indexed evidence.
                                                • specimen category excludes: Biofluid — Meets requirement
                                                  • Supported by the indexed evidence.
                                                  Source metadata
                                                  Source name
                                                  primary colorectal cancer
                                                  Characteristics
                                                  tissue: primary colorectal cancer; ajcc stage: Stage IV
                                                  Description
                                                  Not reported
                                                  Indexed organism evidence
                                                  REPORTED · SAMPLE_REPORTED: Homo sapiens
                                                  Indexed assay evidence
                                                  MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                                                  Source
                                                  GEO
                                                  Original indexed metadata
                                                  sample_accession: GSM1228191
sample_title: primary colorectal cancer AMC_10-1
source_name: primary colorectal cancer
characteristics: tissue: primary colorectal cancer; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                                                  GSM1228192

                                                  Uncertain

                                                  primary colorectal cancer AMC_12-1

                                                  Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Case marker detected.

                                                  Requirements and decision evidence
                                                  • organism: Homo sapiens — Meets requirement
                                                    • Supported by the indexed evidence.
                                                    • organism_evidence_text: Homo sapiens
                                                  • assay type: bulk RNA-seq — Meets requirement
                                                    • Supported by the indexed evidence.
                                                    • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                                                  • specimen category: Tissue or biopsy — Insufficient evidence
                                                    • The required value is not reported.
                                                    • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                                                      • Supported by the indexed evidence.
                                                      • specimen category excludes: Biofluid — Meets requirement
                                                        • Supported by the indexed evidence.
                                                        Source metadata
                                                        Source name
                                                        primary colorectal cancer
                                                        Characteristics
                                                        tissue: primary colorectal cancer; ajcc stage: Stage IV
                                                        Description
                                                        Not reported
                                                        Indexed organism evidence
                                                        REPORTED · SAMPLE_REPORTED: Homo sapiens
                                                        Indexed assay evidence
                                                        MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                                                        Source
                                                        GEO
                                                        Original indexed metadata
                                                        sample_accession: GSM1228192
sample_title: primary colorectal cancer AMC_12-1
source_name: primary colorectal cancer
characteristics: tissue: primary colorectal cancer; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                                                        GSM1228193

                                                        Uncertain

                                                        primary colorectal cancer AMC_13-1

                                                        Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Case marker detected.

                                                        Requirements and decision evidence
                                                        • organism: Homo sapiens — Meets requirement
                                                          • Supported by the indexed evidence.
                                                          • organism_evidence_text: Homo sapiens
                                                        • assay type: bulk RNA-seq — Meets requirement
                                                          • Supported by the indexed evidence.
                                                          • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                                                        • specimen category: Tissue or biopsy — Insufficient evidence
                                                          • The required value is not reported.
                                                          • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                                                            • Supported by the indexed evidence.
                                                            • specimen category excludes: Biofluid — Meets requirement
                                                              • Supported by the indexed evidence.
                                                              Source metadata
                                                              Source name
                                                              primary colorectal cancer
                                                              Characteristics
                                                              tissue: primary colorectal cancer; ajcc stage: Stage IV
                                                              Description
                                                              Not reported
                                                              Indexed organism evidence
                                                              REPORTED · SAMPLE_REPORTED: Homo sapiens
                                                              Indexed assay evidence
                                                              MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                                                              Source
                                                              GEO
                                                              Original indexed metadata
                                                              sample_accession: GSM1228193
sample_title: primary colorectal cancer AMC_13-1
source_name: primary colorectal cancer
characteristics: tissue: primary colorectal cancer; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                                                              GSM1228194

                                                              Uncertain

                                                              primary colorectal cancer AMC_17-1

                                                              Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Case marker detected.

                                                              Requirements and decision evidence
                                                              • organism: Homo sapiens — Meets requirement
                                                                • Supported by the indexed evidence.
                                                                • organism_evidence_text: Homo sapiens
                                                              • assay type: bulk RNA-seq — Meets requirement
                                                                • Supported by the indexed evidence.
                                                                • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                                                              • specimen category: Tissue or biopsy — Insufficient evidence
                                                                • The required value is not reported.
                                                                • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                                                                  • Supported by the indexed evidence.
                                                                  • specimen category excludes: Biofluid — Meets requirement
                                                                    • Supported by the indexed evidence.
                                                                    Source metadata
                                                                    Source name
                                                                    primary colorectal cancer
                                                                    Characteristics
                                                                    tissue: primary colorectal cancer; ajcc stage: Stage IV
                                                                    Description
                                                                    Not reported
                                                                    Indexed organism evidence
                                                                    REPORTED · SAMPLE_REPORTED: Homo sapiens
                                                                    Indexed assay evidence
                                                                    MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                                                                    Source
                                                                    GEO
                                                                    Original indexed metadata
                                                                    sample_accession: GSM1228194
sample_title: primary colorectal cancer AMC_17-1
source_name: primary colorectal cancer
characteristics: tissue: primary colorectal cancer; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                                                                    GSM1228195

                                                                    Uncertain

                                                                    primary colorectal cancer AMC_18-1

                                                                    Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Case marker detected.

                                                                    Requirements and decision evidence
                                                                    • organism: Homo sapiens — Meets requirement
                                                                      • Supported by the indexed evidence.
                                                                      • organism_evidence_text: Homo sapiens
                                                                    • assay type: bulk RNA-seq — Meets requirement
                                                                      • Supported by the indexed evidence.
                                                                      • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                                                                    • specimen category: Tissue or biopsy — Insufficient evidence
                                                                      • The required value is not reported.
                                                                      • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                                                                        • Supported by the indexed evidence.
                                                                        • specimen category excludes: Biofluid — Meets requirement
                                                                          • Supported by the indexed evidence.
                                                                          Source metadata
                                                                          Source name
                                                                          primary colorectal cancer
                                                                          Characteristics
                                                                          tissue: primary colorectal cancer; ajcc stage: Stage IV
                                                                          Description
                                                                          Not reported
                                                                          Indexed organism evidence
                                                                          REPORTED · SAMPLE_REPORTED: Homo sapiens
                                                                          Indexed assay evidence
                                                                          MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                                                                          Source
                                                                          GEO
                                                                          Original indexed metadata
                                                                          sample_accession: GSM1228195
sample_title: primary colorectal cancer AMC_18-1
source_name: primary colorectal cancer
characteristics: tissue: primary colorectal cancer; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                                                                          GSM1228196

                                                                          Uncertain

                                                                          primary colorectal cancer AMC_19-1

                                                                          Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Case marker detected.

                                                                          Requirements and decision evidence
                                                                          • organism: Homo sapiens — Meets requirement
                                                                            • Supported by the indexed evidence.
                                                                            • organism_evidence_text: Homo sapiens
                                                                          • assay type: bulk RNA-seq — Meets requirement
                                                                            • Supported by the indexed evidence.
                                                                            • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                                                                          • specimen category: Tissue or biopsy — Insufficient evidence
                                                                            • The required value is not reported.
                                                                            • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                                                                              • Supported by the indexed evidence.
                                                                              • specimen category excludes: Biofluid — Meets requirement
                                                                                • Supported by the indexed evidence.
                                                                                Source metadata
                                                                                Source name
                                                                                primary colorectal cancer
                                                                                Characteristics
                                                                                tissue: primary colorectal cancer; ajcc stage: Stage IV
                                                                                Description
                                                                                Not reported
                                                                                Indexed organism evidence
                                                                                REPORTED · SAMPLE_REPORTED: Homo sapiens
                                                                                Indexed assay evidence
                                                                                MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                                                                                Source
                                                                                GEO
                                                                                Original indexed metadata
                                                                                sample_accession: GSM1228196
sample_title: primary colorectal cancer AMC_19-1
source_name: primary colorectal cancer
characteristics: tissue: primary colorectal cancer; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                                                                                GSM1228197

                                                                                Uncertain

                                                                                primary colorectal cancer AMC_20-1

                                                                                Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Case marker detected.

                                                                                Requirements and decision evidence
                                                                                • organism: Homo sapiens — Meets requirement
                                                                                  • Supported by the indexed evidence.
                                                                                  • organism_evidence_text: Homo sapiens
                                                                                • assay type: bulk RNA-seq — Meets requirement
                                                                                  • Supported by the indexed evidence.
                                                                                  • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                                                                                • specimen category: Tissue or biopsy — Insufficient evidence
                                                                                  • The required value is not reported.
                                                                                  • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                                                                                    • Supported by the indexed evidence.
                                                                                    • specimen category excludes: Biofluid — Meets requirement
                                                                                      • Supported by the indexed evidence.
                                                                                      Source metadata
                                                                                      Source name
                                                                                      primary colorectal cancer
                                                                                      Characteristics
                                                                                      tissue: primary colorectal cancer; ajcc stage: Stage IV
                                                                                      Description
                                                                                      Not reported
                                                                                      Indexed organism evidence
                                                                                      REPORTED · SAMPLE_REPORTED: Homo sapiens
                                                                                      Indexed assay evidence
                                                                                      MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                                                                                      Source
                                                                                      GEO
                                                                                      Original indexed metadata
                                                                                      sample_accession: GSM1228197
sample_title: primary colorectal cancer AMC_20-1
source_name: primary colorectal cancer
characteristics: tissue: primary colorectal cancer; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                                                                                      GSM1228198

                                                                                      Uncertain

                                                                                      primary colorectal cancer AMC_21-1

                                                                                      Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Case marker detected.

                                                                                      Requirements and decision evidence
                                                                                      • organism: Homo sapiens — Meets requirement
                                                                                        • Supported by the indexed evidence.
                                                                                        • organism_evidence_text: Homo sapiens
                                                                                      • assay type: bulk RNA-seq — Meets requirement
                                                                                        • Supported by the indexed evidence.
                                                                                        • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                                                                                      • specimen category: Tissue or biopsy — Insufficient evidence
                                                                                        • The required value is not reported.
                                                                                        • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                                                                                          • Supported by the indexed evidence.
                                                                                          • specimen category excludes: Biofluid — Meets requirement
                                                                                            • Supported by the indexed evidence.
                                                                                            Source metadata
                                                                                            Source name
                                                                                            primary colorectal cancer
                                                                                            Characteristics
                                                                                            tissue: primary colorectal cancer; ajcc stage: Stage IV
                                                                                            Description
                                                                                            Not reported
                                                                                            Indexed organism evidence
                                                                                            REPORTED · SAMPLE_REPORTED: Homo sapiens
                                                                                            Indexed assay evidence
                                                                                            MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                                                                                            Source
                                                                                            GEO
                                                                                            Original indexed metadata
                                                                                            sample_accession: GSM1228198
sample_title: primary colorectal cancer AMC_21-1
source_name: primary colorectal cancer
characteristics: tissue: primary colorectal cancer; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                                                                                            GSM1228199

                                                                                            Uncertain

                                                                                            primary colorectal cancer AMC_22-1

                                                                                            Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Case marker detected.

                                                                                            Requirements and decision evidence
                                                                                            • organism: Homo sapiens — Meets requirement
                                                                                              • Supported by the indexed evidence.
                                                                                              • organism_evidence_text: Homo sapiens
                                                                                            • assay type: bulk RNA-seq — Meets requirement
                                                                                              • Supported by the indexed evidence.
                                                                                              • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                                                                                            • specimen category: Tissue or biopsy — Insufficient evidence
                                                                                              • The required value is not reported.
                                                                                              • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                                                                                                • Supported by the indexed evidence.
                                                                                                • specimen category excludes: Biofluid — Meets requirement
                                                                                                  • Supported by the indexed evidence.
                                                                                                  Source metadata
                                                                                                  Source name
                                                                                                  primary colorectal cancer
                                                                                                  Characteristics
                                                                                                  tissue: primary colorectal cancer; ajcc stage: Stage IV
                                                                                                  Description
                                                                                                  Not reported
                                                                                                  Indexed organism evidence
                                                                                                  REPORTED · SAMPLE_REPORTED: Homo sapiens
                                                                                                  Indexed assay evidence
                                                                                                  MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                                                                                                  Source
                                                                                                  GEO
                                                                                                  Original indexed metadata
                                                                                                  sample_accession: GSM1228199
sample_title: primary colorectal cancer AMC_22-1
source_name: primary colorectal cancer
characteristics: tissue: primary colorectal cancer; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                                                                                                  GSM1228200

                                                                                                  Uncertain

                                                                                                  primary colorectal cancer AMC_23-1

                                                                                                  Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Case marker detected.

                                                                                                  Requirements and decision evidence
                                                                                                  • organism: Homo sapiens — Meets requirement
                                                                                                    • Supported by the indexed evidence.
                                                                                                    • organism_evidence_text: Homo sapiens
                                                                                                  • assay type: bulk RNA-seq — Meets requirement
                                                                                                    • Supported by the indexed evidence.
                                                                                                    • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                                                                                                  • specimen category: Tissue or biopsy — Insufficient evidence
                                                                                                    • The required value is not reported.
                                                                                                    • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                                                                                                      • Supported by the indexed evidence.
                                                                                                      • specimen category excludes: Biofluid — Meets requirement
                                                                                                        • Supported by the indexed evidence.
                                                                                                        Source metadata
                                                                                                        Source name
                                                                                                        primary colorectal cancer
                                                                                                        Characteristics
                                                                                                        tissue: primary colorectal cancer; ajcc stage: Stage IV
                                                                                                        Description
                                                                                                        Not reported
                                                                                                        Indexed organism evidence
                                                                                                        REPORTED · SAMPLE_REPORTED: Homo sapiens
                                                                                                        Indexed assay evidence
                                                                                                        MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                                                                                                        Source
                                                                                                        GEO
                                                                                                        Original indexed metadata
                                                                                                        sample_accession: GSM1228200
sample_title: primary colorectal cancer AMC_23-1
source_name: primary colorectal cancer
characteristics: tissue: primary colorectal cancer; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                                                                                                        GSM1228201

                                                                                                        Uncertain

                                                                                                        primary colorectal cancer AMC_24-1

                                                                                                        Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Case marker detected.

                                                                                                        Requirements and decision evidence
                                                                                                        • organism: Homo sapiens — Meets requirement
                                                                                                          • Supported by the indexed evidence.
                                                                                                          • organism_evidence_text: Homo sapiens
                                                                                                        • assay type: bulk RNA-seq — Meets requirement
                                                                                                          • Supported by the indexed evidence.
                                                                                                          • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                                                                                                        • specimen category: Tissue or biopsy — Insufficient evidence
                                                                                                          • The required value is not reported.
                                                                                                          • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                                                                                                            • Supported by the indexed evidence.
                                                                                                            • specimen category excludes: Biofluid — Meets requirement
                                                                                                              • Supported by the indexed evidence.
                                                                                                              Source metadata
                                                                                                              Source name
                                                                                                              primary colorectal cancer
                                                                                                              Characteristics
                                                                                                              tissue: primary colorectal cancer; ajcc stage: Stage IV
                                                                                                              Description
                                                                                                              Not reported
                                                                                                              Indexed organism evidence
                                                                                                              REPORTED · SAMPLE_REPORTED: Homo sapiens
                                                                                                              Indexed assay evidence
                                                                                                              MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                                                                                                              Source
                                                                                                              GEO
                                                                                                              Original indexed metadata
                                                                                                              sample_accession: GSM1228201
sample_title: primary colorectal cancer AMC_24-1
source_name: primary colorectal cancer
characteristics: tissue: primary colorectal cancer; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                                                                                                              GSM1228202

                                                                                                              Uncertain

                                                                                                              normal colon AMC_2-2

                                                                                                              Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Sample-local control marker detected.

                                                                                                              Requirements and decision evidence
                                                                                                              • organism: Homo sapiens — Meets requirement
                                                                                                                • Supported by the indexed evidence.
                                                                                                                • organism_evidence_text: Homo sapiens
                                                                                                              • assay type: bulk RNA-seq — Meets requirement
                                                                                                                • Supported by the indexed evidence.
                                                                                                                • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                                                                                                              • specimen category: Tissue or biopsy — Insufficient evidence
                                                                                                                • The required value is not reported.
                                                                                                                • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                                                                                                                  • Supported by the indexed evidence.
                                                                                                                  • specimen category excludes: Biofluid — Meets requirement
                                                                                                                    • Supported by the indexed evidence.
                                                                                                                    Source metadata
                                                                                                                    Source name
                                                                                                                    normal colon
                                                                                                                    Characteristics
                                                                                                                    tissue: normal-looking surrounding colonic epithelium; ajcc stage: Stage IV
                                                                                                                    Description
                                                                                                                    Not reported
                                                                                                                    Indexed organism evidence
                                                                                                                    REPORTED · SAMPLE_REPORTED: Homo sapiens
                                                                                                                    Indexed assay evidence
                                                                                                                    MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                                                                                                                    Source
                                                                                                                    GEO
                                                                                                                    Original indexed metadata
                                                                                                                    sample_accession: GSM1228202
sample_title: normal colon AMC_2-2
source_name: normal colon
characteristics: tissue: normal-looking surrounding colonic epithelium; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                                                                                                                    GSM1228203

                                                                                                                    Uncertain

                                                                                                                    normal colon AMC_3-2

                                                                                                                    Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Sample-local control marker detected.

                                                                                                                    Requirements and decision evidence
                                                                                                                    • organism: Homo sapiens — Meets requirement
                                                                                                                      • Supported by the indexed evidence.
                                                                                                                      • organism_evidence_text: Homo sapiens
                                                                                                                    • assay type: bulk RNA-seq — Meets requirement
                                                                                                                      • Supported by the indexed evidence.
                                                                                                                      • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                                                                                                                    • specimen category: Tissue or biopsy — Insufficient evidence
                                                                                                                      • The required value is not reported.
                                                                                                                      • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                                                                                                                        • Supported by the indexed evidence.
                                                                                                                        • specimen category excludes: Biofluid — Meets requirement
                                                                                                                          • Supported by the indexed evidence.
                                                                                                                          Source metadata
                                                                                                                          Source name
                                                                                                                          normal colon
                                                                                                                          Characteristics
                                                                                                                          tissue: normal-looking surrounding colonic epithelium; ajcc stage: Stage IV
                                                                                                                          Description
                                                                                                                          Not reported
                                                                                                                          Indexed organism evidence
                                                                                                                          REPORTED · SAMPLE_REPORTED: Homo sapiens
                                                                                                                          Indexed assay evidence
                                                                                                                          MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                                                                                                                          Source
                                                                                                                          GEO
                                                                                                                          Original indexed metadata
                                                                                                                          sample_accession: GSM1228203
sample_title: normal colon AMC_3-2
source_name: normal colon
characteristics: tissue: normal-looking surrounding colonic epithelium; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                                                                                                                          GSM1228204

                                                                                                                          Uncertain

                                                                                                                          normal colon AMC_5-2

                                                                                                                          Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Sample-local control marker detected.

                                                                                                                          Requirements and decision evidence
                                                                                                                          • organism: Homo sapiens — Meets requirement
                                                                                                                            • Supported by the indexed evidence.
                                                                                                                            • organism_evidence_text: Homo sapiens
                                                                                                                          • assay type: bulk RNA-seq — Meets requirement
                                                                                                                            • Supported by the indexed evidence.
                                                                                                                            • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                                                                                                                          • specimen category: Tissue or biopsy — Insufficient evidence
                                                                                                                            • The required value is not reported.
                                                                                                                            • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                                                                                                                              • Supported by the indexed evidence.
                                                                                                                              • specimen category excludes: Biofluid — Meets requirement
                                                                                                                                • Supported by the indexed evidence.
                                                                                                                                Source metadata
                                                                                                                                Source name
                                                                                                                                normal colon
                                                                                                                                Characteristics
                                                                                                                                tissue: normal-looking surrounding colonic epithelium; ajcc stage: Stage IV
                                                                                                                                Description
                                                                                                                                Not reported
                                                                                                                                Indexed organism evidence
                                                                                                                                REPORTED · SAMPLE_REPORTED: Homo sapiens
                                                                                                                                Indexed assay evidence
                                                                                                                                MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                                                                                                                                Source
                                                                                                                                GEO
                                                                                                                                Original indexed metadata
                                                                                                                                sample_accession: GSM1228204
sample_title: normal colon AMC_5-2
source_name: normal colon
characteristics: tissue: normal-looking surrounding colonic epithelium; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                                                                                                                                GSM1228205

                                                                                                                                Uncertain

                                                                                                                                normal colon AMC_6-2

                                                                                                                                Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Sample-local control marker detected.

                                                                                                                                Requirements and decision evidence
                                                                                                                                • organism: Homo sapiens — Meets requirement
                                                                                                                                  • Supported by the indexed evidence.
                                                                                                                                  • organism_evidence_text: Homo sapiens
                                                                                                                                • assay type: bulk RNA-seq — Meets requirement
                                                                                                                                  • Supported by the indexed evidence.
                                                                                                                                  • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                                                                                                                                • specimen category: Tissue or biopsy — Insufficient evidence
                                                                                                                                  • The required value is not reported.
                                                                                                                                  • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                                                                                                                                    • Supported by the indexed evidence.
                                                                                                                                    • specimen category excludes: Biofluid — Meets requirement
                                                                                                                                      • Supported by the indexed evidence.
                                                                                                                                      Source metadata
                                                                                                                                      Source name
                                                                                                                                      normal colon
                                                                                                                                      Characteristics
                                                                                                                                      tissue: normal-looking surrounding colonic epithelium; ajcc stage: Stage IV
                                                                                                                                      Description
                                                                                                                                      Not reported
                                                                                                                                      Indexed organism evidence
                                                                                                                                      REPORTED · SAMPLE_REPORTED: Homo sapiens
                                                                                                                                      Indexed assay evidence
                                                                                                                                      MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                                                                                                                                      Source
                                                                                                                                      GEO
                                                                                                                                      Original indexed metadata
                                                                                                                                      sample_accession: GSM1228205
sample_title: normal colon AMC_6-2
source_name: normal colon
characteristics: tissue: normal-looking surrounding colonic epithelium; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                                                                                                                                      GSM1228206

                                                                                                                                      Uncertain

                                                                                                                                      normal colon AMC_7-2

                                                                                                                                      Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Sample-local control marker detected.

                                                                                                                                      Requirements and decision evidence
                                                                                                                                      • organism: Homo sapiens — Meets requirement
                                                                                                                                        • Supported by the indexed evidence.
                                                                                                                                        • organism_evidence_text: Homo sapiens
                                                                                                                                      • assay type: bulk RNA-seq — Meets requirement
                                                                                                                                        • Supported by the indexed evidence.
                                                                                                                                        • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                                                                                                                                      • specimen category: Tissue or biopsy — Insufficient evidence
                                                                                                                                        • The required value is not reported.
                                                                                                                                        • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                                                                                                                                          • Supported by the indexed evidence.
                                                                                                                                          • specimen category excludes: Biofluid — Meets requirement
                                                                                                                                            • Supported by the indexed evidence.
                                                                                                                                            Source metadata
                                                                                                                                            Source name
                                                                                                                                            normal colon
                                                                                                                                            Characteristics
                                                                                                                                            tissue: normal-looking surrounding colonic epithelium; ajcc stage: Stage IV
                                                                                                                                            Description
                                                                                                                                            Not reported
                                                                                                                                            Indexed organism evidence
                                                                                                                                            REPORTED · SAMPLE_REPORTED: Homo sapiens
                                                                                                                                            Indexed assay evidence
                                                                                                                                            MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                                                                                                                                            Source
                                                                                                                                            GEO
                                                                                                                                            Original indexed metadata
                                                                                                                                            sample_accession: GSM1228206
sample_title: normal colon AMC_7-2
source_name: normal colon
characteristics: tissue: normal-looking surrounding colonic epithelium; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                                                                                                                                            GSM1228207

                                                                                                                                            Uncertain

                                                                                                                                            normal colon AMC_8-2

                                                                                                                                            Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Sample-local control marker detected.

                                                                                                                                            Requirements and decision evidence
                                                                                                                                            • organism: Homo sapiens — Meets requirement
                                                                                                                                              • Supported by the indexed evidence.
                                                                                                                                              • organism_evidence_text: Homo sapiens
                                                                                                                                            • assay type: bulk RNA-seq — Meets requirement
                                                                                                                                              • Supported by the indexed evidence.
                                                                                                                                              • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                                                                                                                                            • specimen category: Tissue or biopsy — Insufficient evidence
                                                                                                                                              • The required value is not reported.
                                                                                                                                              • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                                                                                                                                                • Supported by the indexed evidence.
                                                                                                                                                • specimen category excludes: Biofluid — Meets requirement
                                                                                                                                                  • Supported by the indexed evidence.
                                                                                                                                                  Source metadata
                                                                                                                                                  Source name
                                                                                                                                                  normal colon
                                                                                                                                                  Characteristics
                                                                                                                                                  tissue: normal-looking surrounding colonic epithelium; ajcc stage: Stage IV
                                                                                                                                                  Description
                                                                                                                                                  Not reported
                                                                                                                                                  Indexed organism evidence
                                                                                                                                                  REPORTED · SAMPLE_REPORTED: Homo sapiens
                                                                                                                                                  Indexed assay evidence
                                                                                                                                                  MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                                                                                                                                                  Source
                                                                                                                                                  GEO
                                                                                                                                                  Original indexed metadata
                                                                                                                                                  sample_accession: GSM1228207
sample_title: normal colon AMC_8-2
source_name: normal colon
characteristics: tissue: normal-looking surrounding colonic epithelium; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                                                                                                                                                  GSM1228208

                                                                                                                                                  Uncertain

                                                                                                                                                  normal colon AMC_9-2

                                                                                                                                                  Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Sample-local control marker detected.

                                                                                                                                                  Requirements and decision evidence
                                                                                                                                                  • organism: Homo sapiens — Meets requirement
                                                                                                                                                    • Supported by the indexed evidence.
                                                                                                                                                    • organism_evidence_text: Homo sapiens
                                                                                                                                                  • assay type: bulk RNA-seq — Meets requirement
                                                                                                                                                    • Supported by the indexed evidence.
                                                                                                                                                    • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                                                                                                                                                  • specimen category: Tissue or biopsy — Insufficient evidence
                                                                                                                                                    • The required value is not reported.
                                                                                                                                                    • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                                                                                                                                                      • Supported by the indexed evidence.
                                                                                                                                                      • specimen category excludes: Biofluid — Meets requirement
                                                                                                                                                        • Supported by the indexed evidence.
                                                                                                                                                        Source metadata
                                                                                                                                                        Source name
                                                                                                                                                        normal colon
                                                                                                                                                        Characteristics
                                                                                                                                                        tissue: normal-looking surrounding colonic epithelium; ajcc stage: Stage IV
                                                                                                                                                        Description
                                                                                                                                                        Not reported
                                                                                                                                                        Indexed organism evidence
                                                                                                                                                        REPORTED · SAMPLE_REPORTED: Homo sapiens
                                                                                                                                                        Indexed assay evidence
                                                                                                                                                        MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                                                                                                                                                        Source
                                                                                                                                                        GEO
                                                                                                                                                        Original indexed metadata
                                                                                                                                                        sample_accession: GSM1228208
sample_title: normal colon AMC_9-2
source_name: normal colon
characteristics: tissue: normal-looking surrounding colonic epithelium; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                                                                                                                                                        GSM1228209

                                                                                                                                                        Uncertain

                                                                                                                                                        normal colon AMC_10-2

                                                                                                                                                        Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Sample-local control marker detected.

                                                                                                                                                        Requirements and decision evidence
                                                                                                                                                        • organism: Homo sapiens — Meets requirement
                                                                                                                                                          • Supported by the indexed evidence.
                                                                                                                                                          • organism_evidence_text: Homo sapiens
                                                                                                                                                        • assay type: bulk RNA-seq — Meets requirement
                                                                                                                                                          • Supported by the indexed evidence.
                                                                                                                                                          • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                                                                                                                                                        • specimen category: Tissue or biopsy — Insufficient evidence
                                                                                                                                                          • The required value is not reported.
                                                                                                                                                          • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                                                                                                                                                            • Supported by the indexed evidence.
                                                                                                                                                            • specimen category excludes: Biofluid — Meets requirement
                                                                                                                                                              • Supported by the indexed evidence.
                                                                                                                                                              Source metadata
                                                                                                                                                              Source name
                                                                                                                                                              normal colon
                                                                                                                                                              Characteristics
                                                                                                                                                              tissue: normal-looking surrounding colonic epithelium; ajcc stage: Stage IV
                                                                                                                                                              Description
                                                                                                                                                              Not reported
                                                                                                                                                              Indexed organism evidence
                                                                                                                                                              REPORTED · SAMPLE_REPORTED: Homo sapiens
                                                                                                                                                              Indexed assay evidence
                                                                                                                                                              MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                                                                                                                                                              Source
                                                                                                                                                              GEO
                                                                                                                                                              Original indexed metadata
                                                                                                                                                              sample_accession: GSM1228209
sample_title: normal colon AMC_10-2
source_name: normal colon
characteristics: tissue: normal-looking surrounding colonic epithelium; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                                                                                                                                                              GSM1228210

                                                                                                                                                              Uncertain

                                                                                                                                                              normal colon AMC_12-2

                                                                                                                                                              Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Sample-local control marker detected.

                                                                                                                                                              Requirements and decision evidence
                                                                                                                                                              • organism: Homo sapiens — Meets requirement
                                                                                                                                                                • Supported by the indexed evidence.
                                                                                                                                                                • organism_evidence_text: Homo sapiens
                                                                                                                                                              • assay type: bulk RNA-seq — Meets requirement
                                                                                                                                                                • Supported by the indexed evidence.
                                                                                                                                                                • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                                                                                                                                                              • specimen category: Tissue or biopsy — Insufficient evidence
                                                                                                                                                                • The required value is not reported.
                                                                                                                                                                • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                                                                                                                                                                  • Supported by the indexed evidence.
                                                                                                                                                                  • specimen category excludes: Biofluid — Meets requirement
                                                                                                                                                                    • Supported by the indexed evidence.
                                                                                                                                                                    Source metadata
                                                                                                                                                                    Source name
                                                                                                                                                                    normal colon
                                                                                                                                                                    Characteristics
                                                                                                                                                                    tissue: normal-looking surrounding colonic epithelium; ajcc stage: Stage IV
                                                                                                                                                                    Description
                                                                                                                                                                    Not reported
                                                                                                                                                                    Indexed organism evidence
                                                                                                                                                                    REPORTED · SAMPLE_REPORTED: Homo sapiens
                                                                                                                                                                    Indexed assay evidence
                                                                                                                                                                    MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                                                                                                                                                                    Source
                                                                                                                                                                    GEO
                                                                                                                                                                    Original indexed metadata
                                                                                                                                                                    sample_accession: GSM1228210
sample_title: normal colon AMC_12-2
source_name: normal colon
characteristics: tissue: normal-looking surrounding colonic epithelium; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                                                                                                                                                                    GSM1228211

                                                                                                                                                                    Uncertain

                                                                                                                                                                    normal colon AMC_13-2

                                                                                                                                                                    Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Sample-local control marker detected.

                                                                                                                                                                    Requirements and decision evidence
                                                                                                                                                                    • organism: Homo sapiens — Meets requirement
                                                                                                                                                                      • Supported by the indexed evidence.
                                                                                                                                                                      • organism_evidence_text: Homo sapiens
                                                                                                                                                                    • assay type: bulk RNA-seq — Meets requirement
                                                                                                                                                                      • Supported by the indexed evidence.
                                                                                                                                                                      • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                                                                                                                                                                    • specimen category: Tissue or biopsy — Insufficient evidence
                                                                                                                                                                      • The required value is not reported.
                                                                                                                                                                      • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                                                                                                                                                                        • Supported by the indexed evidence.
                                                                                                                                                                        • specimen category excludes: Biofluid — Meets requirement
                                                                                                                                                                          • Supported by the indexed evidence.
                                                                                                                                                                          Source metadata
                                                                                                                                                                          Source name
                                                                                                                                                                          normal colon
                                                                                                                                                                          Characteristics
                                                                                                                                                                          tissue: normal-looking surrounding colonic epithelium; ajcc stage: Stage IV
                                                                                                                                                                          Description
                                                                                                                                                                          Not reported
                                                                                                                                                                          Indexed organism evidence
                                                                                                                                                                          REPORTED · SAMPLE_REPORTED: Homo sapiens
                                                                                                                                                                          Indexed assay evidence
                                                                                                                                                                          MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                                                                                                                                                                          Source
                                                                                                                                                                          GEO
                                                                                                                                                                          Original indexed metadata
                                                                                                                                                                          sample_accession: GSM1228211
sample_title: normal colon AMC_13-2
source_name: normal colon
characteristics: tissue: normal-looking surrounding colonic epithelium; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                                                                                                                                                                          GSM1228212

                                                                                                                                                                          Uncertain

                                                                                                                                                                          normal colon AMC_17-2

                                                                                                                                                                          Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Sample-local control marker detected.

                                                                                                                                                                          Requirements and decision evidence
                                                                                                                                                                          • organism: Homo sapiens — Meets requirement
                                                                                                                                                                            • Supported by the indexed evidence.
                                                                                                                                                                            • organism_evidence_text: Homo sapiens
                                                                                                                                                                          • assay type: bulk RNA-seq — Meets requirement
                                                                                                                                                                            • Supported by the indexed evidence.
                                                                                                                                                                            • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                                                                                                                                                                          • specimen category: Tissue or biopsy — Insufficient evidence
                                                                                                                                                                            • The required value is not reported.
                                                                                                                                                                            • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                                                                                                                                                                              • Supported by the indexed evidence.
                                                                                                                                                                              • specimen category excludes: Biofluid — Meets requirement
                                                                                                                                                                                • Supported by the indexed evidence.
                                                                                                                                                                                Source metadata
                                                                                                                                                                                Source name
                                                                                                                                                                                normal colon
                                                                                                                                                                                Characteristics
                                                                                                                                                                                tissue: normal-looking surrounding colonic epithelium; ajcc stage: Stage IV
                                                                                                                                                                                Description
                                                                                                                                                                                Not reported
                                                                                                                                                                                Indexed organism evidence
                                                                                                                                                                                REPORTED · SAMPLE_REPORTED: Homo sapiens
                                                                                                                                                                                Indexed assay evidence
                                                                                                                                                                                MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                                                                                                                                                                                Source
                                                                                                                                                                                GEO
                                                                                                                                                                                Original indexed metadata
                                                                                                                                                                                sample_accession: GSM1228212
sample_title: normal colon AMC_17-2
source_name: normal colon
characteristics: tissue: normal-looking surrounding colonic epithelium; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                                                                                                                                                                                GSM1228213

                                                                                                                                                                                Uncertain

                                                                                                                                                                                normal colon AMC_18-2

                                                                                                                                                                                Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Sample-local control marker detected.

                                                                                                                                                                                Requirements and decision evidence
                                                                                                                                                                                • organism: Homo sapiens — Meets requirement
                                                                                                                                                                                  • Supported by the indexed evidence.
                                                                                                                                                                                  • organism_evidence_text: Homo sapiens
                                                                                                                                                                                • assay type: bulk RNA-seq — Meets requirement
                                                                                                                                                                                  • Supported by the indexed evidence.
                                                                                                                                                                                  • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                                                                                                                                                                                • specimen category: Tissue or biopsy — Insufficient evidence
                                                                                                                                                                                  • The required value is not reported.
                                                                                                                                                                                  • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                                                                                                                                                                                    • Supported by the indexed evidence.
                                                                                                                                                                                    • specimen category excludes: Biofluid — Meets requirement
                                                                                                                                                                                      • Supported by the indexed evidence.
                                                                                                                                                                                      Source metadata
                                                                                                                                                                                      Source name
                                                                                                                                                                                      normal colon
                                                                                                                                                                                      Characteristics
                                                                                                                                                                                      tissue: normal-looking surrounding colonic epithelium; ajcc stage: Stage IV
                                                                                                                                                                                      Description
                                                                                                                                                                                      Not reported
                                                                                                                                                                                      Indexed organism evidence
                                                                                                                                                                                      REPORTED · SAMPLE_REPORTED: Homo sapiens
                                                                                                                                                                                      Indexed assay evidence
                                                                                                                                                                                      MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                                                                                                                                                                                      Source
                                                                                                                                                                                      GEO
                                                                                                                                                                                      Original indexed metadata
                                                                                                                                                                                      sample_accession: GSM1228213
sample_title: normal colon AMC_18-2
source_name: normal colon
characteristics: tissue: normal-looking surrounding colonic epithelium; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                                                                                                                                                                                      GSM1228214

                                                                                                                                                                                      Uncertain

                                                                                                                                                                                      normal colon AMC_19-2

                                                                                                                                                                                      Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Sample-local control marker detected.

                                                                                                                                                                                      Requirements and decision evidence
                                                                                                                                                                                      • organism: Homo sapiens — Meets requirement
                                                                                                                                                                                        • Supported by the indexed evidence.
                                                                                                                                                                                        • organism_evidence_text: Homo sapiens
                                                                                                                                                                                      • assay type: bulk RNA-seq — Meets requirement
                                                                                                                                                                                        • Supported by the indexed evidence.
                                                                                                                                                                                        • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                                                                                                                                                                                      • specimen category: Tissue or biopsy — Insufficient evidence
                                                                                                                                                                                        • The required value is not reported.
                                                                                                                                                                                        • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                                                                                                                                                                                          • Supported by the indexed evidence.
                                                                                                                                                                                          • specimen category excludes: Biofluid — Meets requirement
                                                                                                                                                                                            • Supported by the indexed evidence.
                                                                                                                                                                                            Source metadata
                                                                                                                                                                                            Source name
                                                                                                                                                                                            normal colon
                                                                                                                                                                                            Characteristics
                                                                                                                                                                                            tissue: normal-looking surrounding colonic epithelium; ajcc stage: Stage IV
                                                                                                                                                                                            Description
                                                                                                                                                                                            Not reported
                                                                                                                                                                                            Indexed organism evidence
                                                                                                                                                                                            REPORTED · SAMPLE_REPORTED: Homo sapiens
                                                                                                                                                                                            Indexed assay evidence
                                                                                                                                                                                            MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                                                                                                                                                                                            Source
                                                                                                                                                                                            GEO
                                                                                                                                                                                            Original indexed metadata
                                                                                                                                                                                            sample_accession: GSM1228214
sample_title: normal colon AMC_19-2
source_name: normal colon
characteristics: tissue: normal-looking surrounding colonic epithelium; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                                                                                                                                                                                            GSM1228215

                                                                                                                                                                                            Uncertain

                                                                                                                                                                                            normal colon AMC_20-2

                                                                                                                                                                                            Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Sample-local control marker detected.

                                                                                                                                                                                            Requirements and decision evidence
                                                                                                                                                                                            • organism: Homo sapiens — Meets requirement
                                                                                                                                                                                              • Supported by the indexed evidence.
                                                                                                                                                                                              • organism_evidence_text: Homo sapiens
                                                                                                                                                                                            • assay type: bulk RNA-seq — Meets requirement
                                                                                                                                                                                              • Supported by the indexed evidence.
                                                                                                                                                                                              • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                                                                                                                                                                                            • specimen category: Tissue or biopsy — Insufficient evidence
                                                                                                                                                                                              • The required value is not reported.
                                                                                                                                                                                              • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                                                                                                                                                                                                • Supported by the indexed evidence.
                                                                                                                                                                                                • specimen category excludes: Biofluid — Meets requirement
                                                                                                                                                                                                  • Supported by the indexed evidence.
                                                                                                                                                                                                  Source metadata
                                                                                                                                                                                                  Source name
                                                                                                                                                                                                  normal colon
                                                                                                                                                                                                  Characteristics
                                                                                                                                                                                                  tissue: normal-looking surrounding colonic epithelium; ajcc stage: Stage IV
                                                                                                                                                                                                  Description
                                                                                                                                                                                                  Not reported
                                                                                                                                                                                                  Indexed organism evidence
                                                                                                                                                                                                  REPORTED · SAMPLE_REPORTED: Homo sapiens
                                                                                                                                                                                                  Indexed assay evidence
                                                                                                                                                                                                  MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                                                                                                                                                                                                  Source
                                                                                                                                                                                                  GEO
                                                                                                                                                                                                  Original indexed metadata
                                                                                                                                                                                                  sample_accession: GSM1228215
sample_title: normal colon AMC_20-2
source_name: normal colon
characteristics: tissue: normal-looking surrounding colonic epithelium; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                                                                                                                                                                                                  GSM1228216

                                                                                                                                                                                                  Uncertain

                                                                                                                                                                                                  normal colon AMC_21-2

                                                                                                                                                                                                  Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Sample-local control marker detected.

                                                                                                                                                                                                  Requirements and decision evidence
                                                                                                                                                                                                  • organism: Homo sapiens — Meets requirement
                                                                                                                                                                                                    • Supported by the indexed evidence.
                                                                                                                                                                                                    • organism_evidence_text: Homo sapiens
                                                                                                                                                                                                  • assay type: bulk RNA-seq — Meets requirement
                                                                                                                                                                                                    • Supported by the indexed evidence.
                                                                                                                                                                                                    • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                                                                                                                                                                                                  • specimen category: Tissue or biopsy — Insufficient evidence
                                                                                                                                                                                                    • The required value is not reported.
                                                                                                                                                                                                    • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                                                                                                                                                                                                      • Supported by the indexed evidence.
                                                                                                                                                                                                      • specimen category excludes: Biofluid — Meets requirement
                                                                                                                                                                                                        • Supported by the indexed evidence.
                                                                                                                                                                                                        Source metadata
                                                                                                                                                                                                        Source name
                                                                                                                                                                                                        normal colon
                                                                                                                                                                                                        Characteristics
                                                                                                                                                                                                        tissue: normal-looking surrounding colonic epithelium; ajcc stage: Stage IV
                                                                                                                                                                                                        Description
                                                                                                                                                                                                        Not reported
                                                                                                                                                                                                        Indexed organism evidence
                                                                                                                                                                                                        REPORTED · SAMPLE_REPORTED: Homo sapiens
                                                                                                                                                                                                        Indexed assay evidence
                                                                                                                                                                                                        MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                                                                                                                                                                                                        Source
                                                                                                                                                                                                        GEO
                                                                                                                                                                                                        Original indexed metadata
                                                                                                                                                                                                        sample_accession: GSM1228216
sample_title: normal colon AMC_21-2
source_name: normal colon
characteristics: tissue: normal-looking surrounding colonic epithelium; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                                                                                                                                                                                                        GSM1228217

                                                                                                                                                                                                        Uncertain

                                                                                                                                                                                                        normal colon AMC_22-2

                                                                                                                                                                                                        Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Sample-local control marker detected.

                                                                                                                                                                                                        Requirements and decision evidence
                                                                                                                                                                                                        • organism: Homo sapiens — Meets requirement
                                                                                                                                                                                                          • Supported by the indexed evidence.
                                                                                                                                                                                                          • organism_evidence_text: Homo sapiens
                                                                                                                                                                                                        • assay type: bulk RNA-seq — Meets requirement
                                                                                                                                                                                                          • Supported by the indexed evidence.
                                                                                                                                                                                                          • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                                                                                                                                                                                                        • specimen category: Tissue or biopsy — Insufficient evidence
                                                                                                                                                                                                          • The required value is not reported.
                                                                                                                                                                                                          • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                                                                                                                                                                                                            • Supported by the indexed evidence.
                                                                                                                                                                                                            • specimen category excludes: Biofluid — Meets requirement
                                                                                                                                                                                                              • Supported by the indexed evidence.
                                                                                                                                                                                                              Source metadata
                                                                                                                                                                                                              Source name
                                                                                                                                                                                                              normal colon
                                                                                                                                                                                                              Characteristics
                                                                                                                                                                                                              tissue: normal-looking surrounding colonic epithelium; ajcc stage: Stage IV
                                                                                                                                                                                                              Description
                                                                                                                                                                                                              Not reported
                                                                                                                                                                                                              Indexed organism evidence
                                                                                                                                                                                                              REPORTED · SAMPLE_REPORTED: Homo sapiens
                                                                                                                                                                                                              Indexed assay evidence
                                                                                                                                                                                                              MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                                                                                                                                                                                                              Source
                                                                                                                                                                                                              GEO
                                                                                                                                                                                                              Original indexed metadata
                                                                                                                                                                                                              sample_accession: GSM1228217
sample_title: normal colon AMC_22-2
source_name: normal colon
characteristics: tissue: normal-looking surrounding colonic epithelium; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                                                                                                                                                                                                              GSM1228218

                                                                                                                                                                                                              Uncertain

                                                                                                                                                                                                              normal colon AMC_23-2

                                                                                                                                                                                                              Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Sample-local control marker detected.

                                                                                                                                                                                                              Requirements and decision evidence
                                                                                                                                                                                                              • organism: Homo sapiens — Meets requirement
                                                                                                                                                                                                                • Supported by the indexed evidence.
                                                                                                                                                                                                                • organism_evidence_text: Homo sapiens
                                                                                                                                                                                                              • assay type: bulk RNA-seq — Meets requirement
                                                                                                                                                                                                                • Supported by the indexed evidence.
                                                                                                                                                                                                                • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                                                                                                                                                                                                              • specimen category: Tissue or biopsy — Insufficient evidence
                                                                                                                                                                                                                • The required value is not reported.
                                                                                                                                                                                                                • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                                                                                                                                                                                                                  • Supported by the indexed evidence.
                                                                                                                                                                                                                  • specimen category excludes: Biofluid — Meets requirement
                                                                                                                                                                                                                    • Supported by the indexed evidence.
                                                                                                                                                                                                                    Source metadata
                                                                                                                                                                                                                    Source name
                                                                                                                                                                                                                    normal colon
                                                                                                                                                                                                                    Characteristics
                                                                                                                                                                                                                    tissue: normal-looking surrounding colonic epithelium; ajcc stage: Stage IV
                                                                                                                                                                                                                    Description
                                                                                                                                                                                                                    Not reported
                                                                                                                                                                                                                    Indexed organism evidence
                                                                                                                                                                                                                    REPORTED · SAMPLE_REPORTED: Homo sapiens
                                                                                                                                                                                                                    Indexed assay evidence
                                                                                                                                                                                                                    MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                                                                                                                                                                                                                    Source
                                                                                                                                                                                                                    GEO
                                                                                                                                                                                                                    Original indexed metadata
                                                                                                                                                                                                                    sample_accession: GSM1228218
sample_title: normal colon AMC_23-2
source_name: normal colon
characteristics: tissue: normal-looking surrounding colonic epithelium; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                                                                                                                                                                                                                    GSM1228219

                                                                                                                                                                                                                    Uncertain

                                                                                                                                                                                                                    normal colon AMC_24-2

                                                                                                                                                                                                                    Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Sample-local control marker detected.

                                                                                                                                                                                                                    Requirements and decision evidence
                                                                                                                                                                                                                    • organism: Homo sapiens — Meets requirement
                                                                                                                                                                                                                      • Supported by the indexed evidence.
                                                                                                                                                                                                                      • organism_evidence_text: Homo sapiens
                                                                                                                                                                                                                    • assay type: bulk RNA-seq — Meets requirement
                                                                                                                                                                                                                      • Supported by the indexed evidence.
                                                                                                                                                                                                                      • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                                                                                                                                                                                                                    • specimen category: Tissue or biopsy — Insufficient evidence
                                                                                                                                                                                                                      • The required value is not reported.
                                                                                                                                                                                                                      • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                                                                                                                                                                                                                        • Supported by the indexed evidence.
                                                                                                                                                                                                                        • specimen category excludes: Biofluid — Meets requirement
                                                                                                                                                                                                                          • Supported by the indexed evidence.
                                                                                                                                                                                                                          Source metadata
                                                                                                                                                                                                                          Source name
                                                                                                                                                                                                                          normal colon
                                                                                                                                                                                                                          Characteristics
                                                                                                                                                                                                                          tissue: normal-looking surrounding colonic epithelium; ajcc stage: Stage IV
                                                                                                                                                                                                                          Description
                                                                                                                                                                                                                          Not reported
                                                                                                                                                                                                                          Indexed organism evidence
                                                                                                                                                                                                                          REPORTED · SAMPLE_REPORTED: Homo sapiens
                                                                                                                                                                                                                          Indexed assay evidence
                                                                                                                                                                                                                          MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                                                                                                                                                                                                                          Source
                                                                                                                                                                                                                          GEO
                                                                                                                                                                                                                          Original indexed metadata
                                                                                                                                                                                                                          sample_accession: GSM1228219
sample_title: normal colon AMC_24-2
source_name: normal colon
characteristics: tissue: normal-looking surrounding colonic epithelium; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                                                                                                                                                                                                                          GSM1228220

                                                                                                                                                                                                                          Uncertain

                                                                                                                                                                                                                          metastasized cancer AMC_2-3

                                                                                                                                                                                                                          Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Case marker detected.

                                                                                                                                                                                                                          Requirements and decision evidence
                                                                                                                                                                                                                          • organism: Homo sapiens — Meets requirement
                                                                                                                                                                                                                            • Supported by the indexed evidence.
                                                                                                                                                                                                                            • organism_evidence_text: Homo sapiens
                                                                                                                                                                                                                          • assay type: bulk RNA-seq — Meets requirement
                                                                                                                                                                                                                            • Supported by the indexed evidence.
                                                                                                                                                                                                                            • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                                                                                                                                                                                                                          • specimen category: Tissue or biopsy — Insufficient evidence
                                                                                                                                                                                                                            • The required value is not reported.
                                                                                                                                                                                                                            • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                                                                                                                                                                                                                              • Supported by the indexed evidence.
                                                                                                                                                                                                                              • specimen category excludes: Biofluid — Meets requirement
                                                                                                                                                                                                                                • Supported by the indexed evidence.
                                                                                                                                                                                                                                Source metadata
                                                                                                                                                                                                                                Source name
                                                                                                                                                                                                                                metastasized cancer
                                                                                                                                                                                                                                Characteristics
                                                                                                                                                                                                                                tissue: metastatic colorectal cancer to the liver; ajcc stage: Stage IV
                                                                                                                                                                                                                                Description
                                                                                                                                                                                                                                Not reported
                                                                                                                                                                                                                                Indexed organism evidence
                                                                                                                                                                                                                                REPORTED · SAMPLE_REPORTED: Homo sapiens
                                                                                                                                                                                                                                Indexed assay evidence
                                                                                                                                                                                                                                MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                                                                                                                                                                                                                                Source
                                                                                                                                                                                                                                GEO
                                                                                                                                                                                                                                Original indexed metadata
                                                                                                                                                                                                                                sample_accession: GSM1228220
sample_title: metastasized cancer AMC_2-3
source_name: metastasized cancer
characteristics: tissue: metastatic colorectal cancer to the liver; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                                                                                                                                                                                                                                GSM1228221

                                                                                                                                                                                                                                Uncertain

                                                                                                                                                                                                                                metastasized cancer AMC_3-3

                                                                                                                                                                                                                                Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Case marker detected.

                                                                                                                                                                                                                                Requirements and decision evidence
                                                                                                                                                                                                                                • organism: Homo sapiens — Meets requirement
                                                                                                                                                                                                                                  • Supported by the indexed evidence.
                                                                                                                                                                                                                                  • organism_evidence_text: Homo sapiens
                                                                                                                                                                                                                                • assay type: bulk RNA-seq — Meets requirement
                                                                                                                                                                                                                                  • Supported by the indexed evidence.
                                                                                                                                                                                                                                  • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                                                                                                                                                                                                                                • specimen category: Tissue or biopsy — Insufficient evidence
                                                                                                                                                                                                                                  • The required value is not reported.
                                                                                                                                                                                                                                  • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                                                                                                                                                                                                                                    • Supported by the indexed evidence.
                                                                                                                                                                                                                                    • specimen category excludes: Biofluid — Meets requirement
                                                                                                                                                                                                                                      • Supported by the indexed evidence.
                                                                                                                                                                                                                                      Source metadata
                                                                                                                                                                                                                                      Source name
                                                                                                                                                                                                                                      metastasized cancer
                                                                                                                                                                                                                                      Characteristics
                                                                                                                                                                                                                                      tissue: metastatic colorectal cancer to the liver; ajcc stage: Stage IV
                                                                                                                                                                                                                                      Description
                                                                                                                                                                                                                                      Not reported
                                                                                                                                                                                                                                      Indexed organism evidence
                                                                                                                                                                                                                                      REPORTED · SAMPLE_REPORTED: Homo sapiens
                                                                                                                                                                                                                                      Indexed assay evidence
                                                                                                                                                                                                                                      MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                                                                                                                                                                                                                                      Source
                                                                                                                                                                                                                                      GEO
                                                                                                                                                                                                                                      Original indexed metadata
                                                                                                                                                                                                                                      sample_accession: GSM1228221
sample_title: metastasized cancer AMC_3-3
source_name: metastasized cancer
characteristics: tissue: metastatic colorectal cancer to the liver; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                                                                                                                                                                                                                                      GSM1228222

                                                                                                                                                                                                                                      Uncertain

                                                                                                                                                                                                                                      metastasized cancer AMC_5-3

                                                                                                                                                                                                                                      Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Case marker detected.

                                                                                                                                                                                                                                      Requirements and decision evidence
                                                                                                                                                                                                                                      • organism: Homo sapiens — Meets requirement
                                                                                                                                                                                                                                        • Supported by the indexed evidence.
                                                                                                                                                                                                                                        • organism_evidence_text: Homo sapiens
                                                                                                                                                                                                                                      • assay type: bulk RNA-seq — Meets requirement
                                                                                                                                                                                                                                        • Supported by the indexed evidence.
                                                                                                                                                                                                                                        • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                                                                                                                                                                                                                                      • specimen category: Tissue or biopsy — Insufficient evidence
                                                                                                                                                                                                                                        • The required value is not reported.
                                                                                                                                                                                                                                        • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                                                                                                                                                                                                                                          • Supported by the indexed evidence.
                                                                                                                                                                                                                                          • specimen category excludes: Biofluid — Meets requirement
                                                                                                                                                                                                                                            • Supported by the indexed evidence.
                                                                                                                                                                                                                                            Source metadata
                                                                                                                                                                                                                                            Source name
                                                                                                                                                                                                                                            metastasized cancer
                                                                                                                                                                                                                                            Characteristics
                                                                                                                                                                                                                                            tissue: metastatic colorectal cancer to the liver; ajcc stage: Stage IV
                                                                                                                                                                                                                                            Description
                                                                                                                                                                                                                                            Not reported
                                                                                                                                                                                                                                            Indexed organism evidence
                                                                                                                                                                                                                                            REPORTED · SAMPLE_REPORTED: Homo sapiens
                                                                                                                                                                                                                                            Indexed assay evidence
                                                                                                                                                                                                                                            MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                                                                                                                                                                                                                                            Source
                                                                                                                                                                                                                                            GEO
                                                                                                                                                                                                                                            Original indexed metadata
                                                                                                                                                                                                                                            sample_accession: GSM1228222
sample_title: metastasized cancer AMC_5-3
source_name: metastasized cancer
characteristics: tissue: metastatic colorectal cancer to the liver; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                                                                                                                                                                                                                                            GSM1228223

                                                                                                                                                                                                                                            Uncertain

                                                                                                                                                                                                                                            metastasized cancer AMC_6-3

                                                                                                                                                                                                                                            Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Case marker detected.

                                                                                                                                                                                                                                            Requirements and decision evidence
                                                                                                                                                                                                                                            • organism: Homo sapiens — Meets requirement
                                                                                                                                                                                                                                              • Supported by the indexed evidence.
                                                                                                                                                                                                                                              • organism_evidence_text: Homo sapiens
                                                                                                                                                                                                                                            • assay type: bulk RNA-seq — Meets requirement
                                                                                                                                                                                                                                              • Supported by the indexed evidence.
                                                                                                                                                                                                                                              • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                                                                                                                                                                                                                                            • specimen category: Tissue or biopsy — Insufficient evidence
                                                                                                                                                                                                                                              • The required value is not reported.
                                                                                                                                                                                                                                              • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                                                                                                                                                                                                                                                • Supported by the indexed evidence.
                                                                                                                                                                                                                                                • specimen category excludes: Biofluid — Meets requirement
                                                                                                                                                                                                                                                  • Supported by the indexed evidence.
                                                                                                                                                                                                                                                  Source metadata
                                                                                                                                                                                                                                                  Source name
                                                                                                                                                                                                                                                  metastasized cancer
                                                                                                                                                                                                                                                  Characteristics
                                                                                                                                                                                                                                                  tissue: metastatic colorectal cancer to the liver; ajcc stage: Stage IV
                                                                                                                                                                                                                                                  Description
                                                                                                                                                                                                                                                  Not reported
                                                                                                                                                                                                                                                  Indexed organism evidence
                                                                                                                                                                                                                                                  REPORTED · SAMPLE_REPORTED: Homo sapiens
                                                                                                                                                                                                                                                  Indexed assay evidence
                                                                                                                                                                                                                                                  MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                                                                                                                                                                                                                                                  Source
                                                                                                                                                                                                                                                  GEO
                                                                                                                                                                                                                                                  Original indexed metadata
                                                                                                                                                                                                                                                  sample_accession: GSM1228223
sample_title: metastasized cancer AMC_6-3
source_name: metastasized cancer
characteristics: tissue: metastatic colorectal cancer to the liver; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                                                                                                                                                                                                                                                  GSM1228224

                                                                                                                                                                                                                                                  Uncertain

                                                                                                                                                                                                                                                  metastasized cancer AMC_7-3

                                                                                                                                                                                                                                                  Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Case marker detected.

                                                                                                                                                                                                                                                  Requirements and decision evidence
                                                                                                                                                                                                                                                  • organism: Homo sapiens — Meets requirement
                                                                                                                                                                                                                                                    • Supported by the indexed evidence.
                                                                                                                                                                                                                                                    • organism_evidence_text: Homo sapiens
                                                                                                                                                                                                                                                  • assay type: bulk RNA-seq — Meets requirement
                                                                                                                                                                                                                                                    • Supported by the indexed evidence.
                                                                                                                                                                                                                                                    • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                                                                                                                                                                                                                                                  • specimen category: Tissue or biopsy — Insufficient evidence
                                                                                                                                                                                                                                                    • The required value is not reported.
                                                                                                                                                                                                                                                    • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                                                                                                                                                                                                                                                      • Supported by the indexed evidence.
                                                                                                                                                                                                                                                      • specimen category excludes: Biofluid — Meets requirement
                                                                                                                                                                                                                                                        • Supported by the indexed evidence.
                                                                                                                                                                                                                                                        Source metadata
                                                                                                                                                                                                                                                        Source name
                                                                                                                                                                                                                                                        metastasized cancer
                                                                                                                                                                                                                                                        Characteristics
                                                                                                                                                                                                                                                        tissue: metastatic colorectal cancer to the liver; ajcc stage: Stage IV
                                                                                                                                                                                                                                                        Description
                                                                                                                                                                                                                                                        Not reported
                                                                                                                                                                                                                                                        Indexed organism evidence
                                                                                                                                                                                                                                                        REPORTED · SAMPLE_REPORTED: Homo sapiens
                                                                                                                                                                                                                                                        Indexed assay evidence
                                                                                                                                                                                                                                                        MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                                                                                                                                                                                                                                                        Source
                                                                                                                                                                                                                                                        GEO
                                                                                                                                                                                                                                                        Original indexed metadata
                                                                                                                                                                                                                                                        sample_accession: GSM1228224
sample_title: metastasized cancer AMC_7-3
source_name: metastasized cancer
characteristics: tissue: metastatic colorectal cancer to the liver; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                                                                                                                                                                                                                                                        GSM1228225

                                                                                                                                                                                                                                                        Uncertain

                                                                                                                                                                                                                                                        metastasized cancer AMC_8-3

                                                                                                                                                                                                                                                        Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Case marker detected.

                                                                                                                                                                                                                                                        Requirements and decision evidence
                                                                                                                                                                                                                                                        • organism: Homo sapiens — Meets requirement
                                                                                                                                                                                                                                                          • Supported by the indexed evidence.
                                                                                                                                                                                                                                                          • organism_evidence_text: Homo sapiens
                                                                                                                                                                                                                                                        • assay type: bulk RNA-seq — Meets requirement
                                                                                                                                                                                                                                                          • Supported by the indexed evidence.
                                                                                                                                                                                                                                                          • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                                                                                                                                                                                                                                                        • specimen category: Tissue or biopsy — Insufficient evidence
                                                                                                                                                                                                                                                          • The required value is not reported.
                                                                                                                                                                                                                                                          • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                                                                                                                                                                                                                                                            • Supported by the indexed evidence.
                                                                                                                                                                                                                                                            • specimen category excludes: Biofluid — Meets requirement
                                                                                                                                                                                                                                                              • Supported by the indexed evidence.
                                                                                                                                                                                                                                                              Source metadata
                                                                                                                                                                                                                                                              Source name
                                                                                                                                                                                                                                                              metastasized cancer
                                                                                                                                                                                                                                                              Characteristics
                                                                                                                                                                                                                                                              tissue: metastatic colorectal cancer to the liver; ajcc stage: Stage IV
                                                                                                                                                                                                                                                              Description
                                                                                                                                                                                                                                                              Not reported
                                                                                                                                                                                                                                                              Indexed organism evidence
                                                                                                                                                                                                                                                              REPORTED · SAMPLE_REPORTED: Homo sapiens
                                                                                                                                                                                                                                                              Indexed assay evidence
                                                                                                                                                                                                                                                              MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                                                                                                                                                                                                                                                              Source
                                                                                                                                                                                                                                                              GEO
                                                                                                                                                                                                                                                              Original indexed metadata
                                                                                                                                                                                                                                                              sample_accession: GSM1228225
sample_title: metastasized cancer AMC_8-3
source_name: metastasized cancer
characteristics: tissue: metastatic colorectal cancer to the liver; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                                                                                                                                                                                                                                                              GSM1228226

                                                                                                                                                                                                                                                              Uncertain

                                                                                                                                                                                                                                                              metastasized cancer AMC_9-3

                                                                                                                                                                                                                                                              Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Case marker detected.

                                                                                                                                                                                                                                                              Requirements and decision evidence
                                                                                                                                                                                                                                                              • organism: Homo sapiens — Meets requirement
                                                                                                                                                                                                                                                                • Supported by the indexed evidence.
                                                                                                                                                                                                                                                                • organism_evidence_text: Homo sapiens
                                                                                                                                                                                                                                                              • assay type: bulk RNA-seq — Meets requirement
                                                                                                                                                                                                                                                                • Supported by the indexed evidence.
                                                                                                                                                                                                                                                                • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                                                                                                                                                                                                                                                              • specimen category: Tissue or biopsy — Insufficient evidence
                                                                                                                                                                                                                                                                • The required value is not reported.
                                                                                                                                                                                                                                                                • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                                                                                                                                                                                                                                                                  • Supported by the indexed evidence.
                                                                                                                                                                                                                                                                  • specimen category excludes: Biofluid — Meets requirement
                                                                                                                                                                                                                                                                    • Supported by the indexed evidence.
                                                                                                                                                                                                                                                                    Source metadata
                                                                                                                                                                                                                                                                    Source name
                                                                                                                                                                                                                                                                    metastasized cancer
                                                                                                                                                                                                                                                                    Characteristics
                                                                                                                                                                                                                                                                    tissue: metastatic colorectal cancer to the liver; ajcc stage: Stage IV
                                                                                                                                                                                                                                                                    Description
                                                                                                                                                                                                                                                                    Not reported
                                                                                                                                                                                                                                                                    Indexed organism evidence
                                                                                                                                                                                                                                                                    REPORTED · SAMPLE_REPORTED: Homo sapiens
                                                                                                                                                                                                                                                                    Indexed assay evidence
                                                                                                                                                                                                                                                                    MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                                                                                                                                                                                                                                                                    Source
                                                                                                                                                                                                                                                                    GEO
                                                                                                                                                                                                                                                                    Original indexed metadata
                                                                                                                                                                                                                                                                    sample_accession: GSM1228226
sample_title: metastasized cancer AMC_9-3
source_name: metastasized cancer
characteristics: tissue: metastatic colorectal cancer to the liver; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                                                                                                                                                                                                                                                                    GSM1228227

                                                                                                                                                                                                                                                                    Uncertain

                                                                                                                                                                                                                                                                    metastasized cancer AMC_10-3

                                                                                                                                                                                                                                                                    Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Case marker detected.

                                                                                                                                                                                                                                                                    Requirements and decision evidence
                                                                                                                                                                                                                                                                    • organism: Homo sapiens — Meets requirement
                                                                                                                                                                                                                                                                      • Supported by the indexed evidence.
                                                                                                                                                                                                                                                                      • organism_evidence_text: Homo sapiens
                                                                                                                                                                                                                                                                    • assay type: bulk RNA-seq — Meets requirement
                                                                                                                                                                                                                                                                      • Supported by the indexed evidence.
                                                                                                                                                                                                                                                                      • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                                                                                                                                                                                                                                                                    • specimen category: Tissue or biopsy — Insufficient evidence
                                                                                                                                                                                                                                                                      • The required value is not reported.
                                                                                                                                                                                                                                                                      • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                                                                                                                                                                                                                                                                        • Supported by the indexed evidence.
                                                                                                                                                                                                                                                                        • specimen category excludes: Biofluid — Meets requirement
                                                                                                                                                                                                                                                                          • Supported by the indexed evidence.
                                                                                                                                                                                                                                                                          Source metadata
                                                                                                                                                                                                                                                                          Source name
                                                                                                                                                                                                                                                                          metastasized cancer
                                                                                                                                                                                                                                                                          Characteristics
                                                                                                                                                                                                                                                                          tissue: metastatic colorectal cancer to the liver; ajcc stage: Stage IV
                                                                                                                                                                                                                                                                          Description
                                                                                                                                                                                                                                                                          Not reported
                                                                                                                                                                                                                                                                          Indexed organism evidence
                                                                                                                                                                                                                                                                          REPORTED · SAMPLE_REPORTED: Homo sapiens
                                                                                                                                                                                                                                                                          Indexed assay evidence
                                                                                                                                                                                                                                                                          MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                                                                                                                                                                                                                                                                          Source
                                                                                                                                                                                                                                                                          GEO
                                                                                                                                                                                                                                                                          Original indexed metadata
                                                                                                                                                                                                                                                                          sample_accession: GSM1228227
sample_title: metastasized cancer AMC_10-3
source_name: metastasized cancer
characteristics: tissue: metastatic colorectal cancer to the liver; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                                                                                                                                                                                                                                                                          GSM1228228

                                                                                                                                                                                                                                                                          Uncertain

                                                                                                                                                                                                                                                                          metastasized cancer AMC_12-3

                                                                                                                                                                                                                                                                          Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Case marker detected.

                                                                                                                                                                                                                                                                          Requirements and decision evidence
                                                                                                                                                                                                                                                                          • organism: Homo sapiens — Meets requirement
                                                                                                                                                                                                                                                                            • Supported by the indexed evidence.
                                                                                                                                                                                                                                                                            • organism_evidence_text: Homo sapiens
                                                                                                                                                                                                                                                                          • assay type: bulk RNA-seq — Meets requirement
                                                                                                                                                                                                                                                                            • Supported by the indexed evidence.
                                                                                                                                                                                                                                                                            • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                                                                                                                                                                                                                                                                          • specimen category: Tissue or biopsy — Insufficient evidence
                                                                                                                                                                                                                                                                            • The required value is not reported.
                                                                                                                                                                                                                                                                            • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                                                                                                                                                                                                                                                                              • Supported by the indexed evidence.
                                                                                                                                                                                                                                                                              • specimen category excludes: Biofluid — Meets requirement
                                                                                                                                                                                                                                                                                • Supported by the indexed evidence.
                                                                                                                                                                                                                                                                                Source metadata
                                                                                                                                                                                                                                                                                Source name
                                                                                                                                                                                                                                                                                metastasized cancer
                                                                                                                                                                                                                                                                                Characteristics
                                                                                                                                                                                                                                                                                tissue: metastatic colorectal cancer to the liver; ajcc stage: Stage IV
                                                                                                                                                                                                                                                                                Description
                                                                                                                                                                                                                                                                                Not reported
                                                                                                                                                                                                                                                                                Indexed organism evidence
                                                                                                                                                                                                                                                                                REPORTED · SAMPLE_REPORTED: Homo sapiens
                                                                                                                                                                                                                                                                                Indexed assay evidence
                                                                                                                                                                                                                                                                                MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                                                                                                                                                                                                                                                                                Source
                                                                                                                                                                                                                                                                                GEO
                                                                                                                                                                                                                                                                                Original indexed metadata
                                                                                                                                                                                                                                                                                sample_accession: GSM1228228
sample_title: metastasized cancer AMC_12-3
source_name: metastasized cancer
characteristics: tissue: metastatic colorectal cancer to the liver; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                                                                                                                                                                                                                                                                                GSM1228229

                                                                                                                                                                                                                                                                                Uncertain

                                                                                                                                                                                                                                                                                metastasized cancer AMC_13-3

                                                                                                                                                                                                                                                                                Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Case marker detected.

                                                                                                                                                                                                                                                                                Requirements and decision evidence
                                                                                                                                                                                                                                                                                • organism: Homo sapiens — Meets requirement
                                                                                                                                                                                                                                                                                  • Supported by the indexed evidence.
                                                                                                                                                                                                                                                                                  • organism_evidence_text: Homo sapiens
                                                                                                                                                                                                                                                                                • assay type: bulk RNA-seq — Meets requirement
                                                                                                                                                                                                                                                                                  • Supported by the indexed evidence.
                                                                                                                                                                                                                                                                                  • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                                                                                                                                                                                                                                                                                • specimen category: Tissue or biopsy — Insufficient evidence
                                                                                                                                                                                                                                                                                  • The required value is not reported.
                                                                                                                                                                                                                                                                                  • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                                                                                                                                                                                                                                                                                    • Supported by the indexed evidence.
                                                                                                                                                                                                                                                                                    • specimen category excludes: Biofluid — Meets requirement
                                                                                                                                                                                                                                                                                      • Supported by the indexed evidence.
                                                                                                                                                                                                                                                                                      Source metadata
                                                                                                                                                                                                                                                                                      Source name
                                                                                                                                                                                                                                                                                      metastasized cancer
                                                                                                                                                                                                                                                                                      Characteristics
                                                                                                                                                                                                                                                                                      tissue: metastatic colorectal cancer to the liver; ajcc stage: Stage IV
                                                                                                                                                                                                                                                                                      Description
                                                                                                                                                                                                                                                                                      Not reported
                                                                                                                                                                                                                                                                                      Indexed organism evidence
                                                                                                                                                                                                                                                                                      REPORTED · SAMPLE_REPORTED: Homo sapiens
                                                                                                                                                                                                                                                                                      Indexed assay evidence
                                                                                                                                                                                                                                                                                      MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                                                                                                                                                                                                                                                                                      Source
                                                                                                                                                                                                                                                                                      GEO
                                                                                                                                                                                                                                                                                      Original indexed metadata
                                                                                                                                                                                                                                                                                      sample_accession: GSM1228229
sample_title: metastasized cancer AMC_13-3
source_name: metastasized cancer
characteristics: tissue: metastatic colorectal cancer to the liver; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                                                                                                                                                                                                                                                                                      GSM1228230

                                                                                                                                                                                                                                                                                      Uncertain

                                                                                                                                                                                                                                                                                      metastasized cancer AMC_17-3

                                                                                                                                                                                                                                                                                      Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Case marker detected.

                                                                                                                                                                                                                                                                                      Requirements and decision evidence
                                                                                                                                                                                                                                                                                      • organism: Homo sapiens — Meets requirement
                                                                                                                                                                                                                                                                                        • Supported by the indexed evidence.
                                                                                                                                                                                                                                                                                        • organism_evidence_text: Homo sapiens
                                                                                                                                                                                                                                                                                      • assay type: bulk RNA-seq — Meets requirement
                                                                                                                                                                                                                                                                                        • Supported by the indexed evidence.
                                                                                                                                                                                                                                                                                        • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                                                                                                                                                                                                                                                                                      • specimen category: Tissue or biopsy — Insufficient evidence
                                                                                                                                                                                                                                                                                        • The required value is not reported.
                                                                                                                                                                                                                                                                                        • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                                                                                                                                                                                                                                                                                          • Supported by the indexed evidence.
                                                                                                                                                                                                                                                                                          • specimen category excludes: Biofluid — Meets requirement
                                                                                                                                                                                                                                                                                            • Supported by the indexed evidence.
                                                                                                                                                                                                                                                                                            Source metadata
                                                                                                                                                                                                                                                                                            Source name
                                                                                                                                                                                                                                                                                            metastasized cancer
                                                                                                                                                                                                                                                                                            Characteristics
                                                                                                                                                                                                                                                                                            tissue: metastatic colorectal cancer to the liver; ajcc stage: Stage IV
                                                                                                                                                                                                                                                                                            Description
                                                                                                                                                                                                                                                                                            Not reported
                                                                                                                                                                                                                                                                                            Indexed organism evidence
                                                                                                                                                                                                                                                                                            REPORTED · SAMPLE_REPORTED: Homo sapiens
                                                                                                                                                                                                                                                                                            Indexed assay evidence
                                                                                                                                                                                                                                                                                            MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                                                                                                                                                                                                                                                                                            Source
                                                                                                                                                                                                                                                                                            GEO
                                                                                                                                                                                                                                                                                            Original indexed metadata
                                                                                                                                                                                                                                                                                            sample_accession: GSM1228230
sample_title: metastasized cancer AMC_17-3
source_name: metastasized cancer
characteristics: tissue: metastatic colorectal cancer to the liver; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                                                                                                                                                                                                                                                                                            GSM1228231

                                                                                                                                                                                                                                                                                            Uncertain

                                                                                                                                                                                                                                                                                            metastasized cancer AMC_18-3

                                                                                                                                                                                                                                                                                            Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Case marker detected.

                                                                                                                                                                                                                                                                                            Requirements and decision evidence
                                                                                                                                                                                                                                                                                            • organism: Homo sapiens — Meets requirement
                                                                                                                                                                                                                                                                                              • Supported by the indexed evidence.
                                                                                                                                                                                                                                                                                              • organism_evidence_text: Homo sapiens
                                                                                                                                                                                                                                                                                            • assay type: bulk RNA-seq — Meets requirement
                                                                                                                                                                                                                                                                                              • Supported by the indexed evidence.
                                                                                                                                                                                                                                                                                              • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                                                                                                                                                                                                                                                                                            • specimen category: Tissue or biopsy — Insufficient evidence
                                                                                                                                                                                                                                                                                              • The required value is not reported.
                                                                                                                                                                                                                                                                                              • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                                                                                                                                                                                                                                                                                                • Supported by the indexed evidence.
                                                                                                                                                                                                                                                                                                • specimen category excludes: Biofluid — Meets requirement
                                                                                                                                                                                                                                                                                                  • Supported by the indexed evidence.
                                                                                                                                                                                                                                                                                                  Source metadata
                                                                                                                                                                                                                                                                                                  Source name
                                                                                                                                                                                                                                                                                                  metastasized cancer
                                                                                                                                                                                                                                                                                                  Characteristics
                                                                                                                                                                                                                                                                                                  tissue: metastatic colorectal cancer to the liver; ajcc stage: Stage IV
                                                                                                                                                                                                                                                                                                  Description
                                                                                                                                                                                                                                                                                                  Not reported
                                                                                                                                                                                                                                                                                                  Indexed organism evidence
                                                                                                                                                                                                                                                                                                  REPORTED · SAMPLE_REPORTED: Homo sapiens
                                                                                                                                                                                                                                                                                                  Indexed assay evidence
                                                                                                                                                                                                                                                                                                  MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                                                                                                                                                                                                                                                                                                  Source
                                                                                                                                                                                                                                                                                                  GEO
                                                                                                                                                                                                                                                                                                  Original indexed metadata
                                                                                                                                                                                                                                                                                                  sample_accession: GSM1228231
sample_title: metastasized cancer AMC_18-3
source_name: metastasized cancer
characteristics: tissue: metastatic colorectal cancer to the liver; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                                                                                                                                                                                                                                                                                                  GSM1228232

                                                                                                                                                                                                                                                                                                  Uncertain

                                                                                                                                                                                                                                                                                                  metastasized cancer AMC_19-3

                                                                                                                                                                                                                                                                                                  Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Case marker detected.

                                                                                                                                                                                                                                                                                                  Requirements and decision evidence
                                                                                                                                                                                                                                                                                                  • organism: Homo sapiens — Meets requirement
                                                                                                                                                                                                                                                                                                    • Supported by the indexed evidence.
                                                                                                                                                                                                                                                                                                    • organism_evidence_text: Homo sapiens
                                                                                                                                                                                                                                                                                                  • assay type: bulk RNA-seq — Meets requirement
                                                                                                                                                                                                                                                                                                    • Supported by the indexed evidence.
                                                                                                                                                                                                                                                                                                    • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                                                                                                                                                                                                                                                                                                  • specimen category: Tissue or biopsy — Insufficient evidence
                                                                                                                                                                                                                                                                                                    • The required value is not reported.
                                                                                                                                                                                                                                                                                                    • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                                                                                                                                                                                                                                                                                                      • Supported by the indexed evidence.
                                                                                                                                                                                                                                                                                                      • specimen category excludes: Biofluid — Meets requirement
                                                                                                                                                                                                                                                                                                        • Supported by the indexed evidence.
                                                                                                                                                                                                                                                                                                        Source metadata
                                                                                                                                                                                                                                                                                                        Source name
                                                                                                                                                                                                                                                                                                        metastasized cancer
                                                                                                                                                                                                                                                                                                        Characteristics
                                                                                                                                                                                                                                                                                                        tissue: metastatic colorectal cancer to the liver; ajcc stage: Stage IV
                                                                                                                                                                                                                                                                                                        Description
                                                                                                                                                                                                                                                                                                        Not reported
                                                                                                                                                                                                                                                                                                        Indexed organism evidence
                                                                                                                                                                                                                                                                                                        REPORTED · SAMPLE_REPORTED: Homo sapiens
                                                                                                                                                                                                                                                                                                        Indexed assay evidence
                                                                                                                                                                                                                                                                                                        MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                                                                                                                                                                                                                                                                                                        Source
                                                                                                                                                                                                                                                                                                        GEO
                                                                                                                                                                                                                                                                                                        Original indexed metadata
                                                                                                                                                                                                                                                                                                        sample_accession: GSM1228232
sample_title: metastasized cancer AMC_19-3
source_name: metastasized cancer
characteristics: tissue: metastatic colorectal cancer to the liver; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                                                                                                                                                                                                                                                                                                        GSM1228233

                                                                                                                                                                                                                                                                                                        Uncertain

                                                                                                                                                                                                                                                                                                        metastasized cancer AMC_20-3

                                                                                                                                                                                                                                                                                                        Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Case marker detected.

                                                                                                                                                                                                                                                                                                        Requirements and decision evidence
                                                                                                                                                                                                                                                                                                        • organism: Homo sapiens — Meets requirement
                                                                                                                                                                                                                                                                                                          • Supported by the indexed evidence.
                                                                                                                                                                                                                                                                                                          • organism_evidence_text: Homo sapiens
                                                                                                                                                                                                                                                                                                        • assay type: bulk RNA-seq — Meets requirement
                                                                                                                                                                                                                                                                                                          • Supported by the indexed evidence.
                                                                                                                                                                                                                                                                                                          • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                                                                                                                                                                                                                                                                                                        • specimen category: Tissue or biopsy — Insufficient evidence
                                                                                                                                                                                                                                                                                                          • The required value is not reported.
                                                                                                                                                                                                                                                                                                          • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                                                                                                                                                                                                                                                                                                            • Supported by the indexed evidence.
                                                                                                                                                                                                                                                                                                            • specimen category excludes: Biofluid — Meets requirement
                                                                                                                                                                                                                                                                                                              • Supported by the indexed evidence.
                                                                                                                                                                                                                                                                                                              Source metadata
                                                                                                                                                                                                                                                                                                              Source name
                                                                                                                                                                                                                                                                                                              metastasized cancer
                                                                                                                                                                                                                                                                                                              Characteristics
                                                                                                                                                                                                                                                                                                              tissue: metastatic colorectal cancer to the liver; ajcc stage: Stage IV
                                                                                                                                                                                                                                                                                                              Description
                                                                                                                                                                                                                                                                                                              Not reported
                                                                                                                                                                                                                                                                                                              Indexed organism evidence
                                                                                                                                                                                                                                                                                                              REPORTED · SAMPLE_REPORTED: Homo sapiens
                                                                                                                                                                                                                                                                                                              Indexed assay evidence
                                                                                                                                                                                                                                                                                                              MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                                                                                                                                                                                                                                                                                                              Source
                                                                                                                                                                                                                                                                                                              GEO
                                                                                                                                                                                                                                                                                                              Original indexed metadata
                                                                                                                                                                                                                                                                                                              sample_accession: GSM1228233
sample_title: metastasized cancer AMC_20-3
source_name: metastasized cancer
characteristics: tissue: metastatic colorectal cancer to the liver; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                                                                                                                                                                                                                                                                                                              GSM1228234

                                                                                                                                                                                                                                                                                                              Uncertain

                                                                                                                                                                                                                                                                                                              metastasized cancer AMC_21-3

                                                                                                                                                                                                                                                                                                              Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Case marker detected.

                                                                                                                                                                                                                                                                                                              Requirements and decision evidence
                                                                                                                                                                                                                                                                                                              • organism: Homo sapiens — Meets requirement
                                                                                                                                                                                                                                                                                                                • Supported by the indexed evidence.
                                                                                                                                                                                                                                                                                                                • organism_evidence_text: Homo sapiens
                                                                                                                                                                                                                                                                                                              • assay type: bulk RNA-seq — Meets requirement
                                                                                                                                                                                                                                                                                                                • Supported by the indexed evidence.
                                                                                                                                                                                                                                                                                                                • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                                                                                                                                                                                                                                                                                                              • specimen category: Tissue or biopsy — Insufficient evidence
                                                                                                                                                                                                                                                                                                                • The required value is not reported.
                                                                                                                                                                                                                                                                                                                • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                                                                                                                                                                                                                                                                                                                  • Supported by the indexed evidence.
                                                                                                                                                                                                                                                                                                                  • specimen category excludes: Biofluid — Meets requirement
                                                                                                                                                                                                                                                                                                                    • Supported by the indexed evidence.
                                                                                                                                                                                                                                                                                                                    Source metadata
                                                                                                                                                                                                                                                                                                                    Source name
                                                                                                                                                                                                                                                                                                                    metastasized cancer
                                                                                                                                                                                                                                                                                                                    Characteristics
                                                                                                                                                                                                                                                                                                                    tissue: metastatic colorectal cancer to the liver; ajcc stage: Stage IV
                                                                                                                                                                                                                                                                                                                    Description
                                                                                                                                                                                                                                                                                                                    Not reported
                                                                                                                                                                                                                                                                                                                    Indexed organism evidence
                                                                                                                                                                                                                                                                                                                    REPORTED · SAMPLE_REPORTED: Homo sapiens
                                                                                                                                                                                                                                                                                                                    Indexed assay evidence
                                                                                                                                                                                                                                                                                                                    MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                                                                                                                                                                                                                                                                                                                    Source
                                                                                                                                                                                                                                                                                                                    GEO
                                                                                                                                                                                                                                                                                                                    Original indexed metadata
                                                                                                                                                                                                                                                                                                                    sample_accession: GSM1228234
sample_title: metastasized cancer AMC_21-3
source_name: metastasized cancer
characteristics: tissue: metastatic colorectal cancer to the liver; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                                                                                                                                                                                                                                                                                                                    GSM1228235

                                                                                                                                                                                                                                                                                                                    Uncertain

                                                                                                                                                                                                                                                                                                                    metastasized cancer AMC_22-3

                                                                                                                                                                                                                                                                                                                    Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Case marker detected.

                                                                                                                                                                                                                                                                                                                    Requirements and decision evidence
                                                                                                                                                                                                                                                                                                                    • organism: Homo sapiens — Meets requirement
                                                                                                                                                                                                                                                                                                                      • Supported by the indexed evidence.
                                                                                                                                                                                                                                                                                                                      • organism_evidence_text: Homo sapiens
                                                                                                                                                                                                                                                                                                                    • assay type: bulk RNA-seq — Meets requirement
                                                                                                                                                                                                                                                                                                                      • Supported by the indexed evidence.
                                                                                                                                                                                                                                                                                                                      • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                                                                                                                                                                                                                                                                                                                    • specimen category: Tissue or biopsy — Insufficient evidence
                                                                                                                                                                                                                                                                                                                      • The required value is not reported.
                                                                                                                                                                                                                                                                                                                      • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                                                                                                                                                                                                                                                                                                                        • Supported by the indexed evidence.
                                                                                                                                                                                                                                                                                                                        • specimen category excludes: Biofluid — Meets requirement
                                                                                                                                                                                                                                                                                                                          • Supported by the indexed evidence.
                                                                                                                                                                                                                                                                                                                          Source metadata
                                                                                                                                                                                                                                                                                                                          Source name
                                                                                                                                                                                                                                                                                                                          metastasized cancer
                                                                                                                                                                                                                                                                                                                          Characteristics
                                                                                                                                                                                                                                                                                                                          tissue: metastatic colorectal cancer to the liver; ajcc stage: Stage IV
                                                                                                                                                                                                                                                                                                                          Description
                                                                                                                                                                                                                                                                                                                          Not reported
                                                                                                                                                                                                                                                                                                                          Indexed organism evidence
                                                                                                                                                                                                                                                                                                                          REPORTED · SAMPLE_REPORTED: Homo sapiens
                                                                                                                                                                                                                                                                                                                          Indexed assay evidence
                                                                                                                                                                                                                                                                                                                          MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                                                                                                                                                                                                                                                                                                                          Source
                                                                                                                                                                                                                                                                                                                          GEO
                                                                                                                                                                                                                                                                                                                          Original indexed metadata
                                                                                                                                                                                                                                                                                                                          sample_accession: GSM1228235
sample_title: metastasized cancer AMC_22-3
source_name: metastasized cancer
characteristics: tissue: metastatic colorectal cancer to the liver; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                                                                                                                                                                                                                                                                                                                          GSM1228236

                                                                                                                                                                                                                                                                                                                          Uncertain

                                                                                                                                                                                                                                                                                                                          metastasized cancer AMC_23-3

                                                                                                                                                                                                                                                                                                                          Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Case marker detected.

                                                                                                                                                                                                                                                                                                                          Requirements and decision evidence
                                                                                                                                                                                                                                                                                                                          • organism: Homo sapiens — Meets requirement
                                                                                                                                                                                                                                                                                                                            • Supported by the indexed evidence.
                                                                                                                                                                                                                                                                                                                            • organism_evidence_text: Homo sapiens
                                                                                                                                                                                                                                                                                                                          • assay type: bulk RNA-seq — Meets requirement
                                                                                                                                                                                                                                                                                                                            • Supported by the indexed evidence.
                                                                                                                                                                                                                                                                                                                            • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                                                                                                                                                                                                                                                                                                                          • specimen category: Tissue or biopsy — Insufficient evidence
                                                                                                                                                                                                                                                                                                                            • The required value is not reported.
                                                                                                                                                                                                                                                                                                                            • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                                                                                                                                                                                                                                                                                                                              • Supported by the indexed evidence.
                                                                                                                                                                                                                                                                                                                              • specimen category excludes: Biofluid — Meets requirement
                                                                                                                                                                                                                                                                                                                                • Supported by the indexed evidence.
                                                                                                                                                                                                                                                                                                                                Source metadata
                                                                                                                                                                                                                                                                                                                                Source name
                                                                                                                                                                                                                                                                                                                                metastasized cancer
                                                                                                                                                                                                                                                                                                                                Characteristics
                                                                                                                                                                                                                                                                                                                                tissue: metastatic colorectal cancer to the liver; ajcc stage: Stage IV
                                                                                                                                                                                                                                                                                                                                Description
                                                                                                                                                                                                                                                                                                                                Not reported
                                                                                                                                                                                                                                                                                                                                Indexed organism evidence
                                                                                                                                                                                                                                                                                                                                REPORTED · SAMPLE_REPORTED: Homo sapiens
                                                                                                                                                                                                                                                                                                                                Indexed assay evidence
                                                                                                                                                                                                                                                                                                                                MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                                                                                                                                                                                                                                                                                                                                Source
                                                                                                                                                                                                                                                                                                                                GEO
                                                                                                                                                                                                                                                                                                                                Original indexed metadata
                                                                                                                                                                                                                                                                                                                                sample_accession: GSM1228236
sample_title: metastasized cancer AMC_23-3
source_name: metastasized cancer
characteristics: tissue: metastatic colorectal cancer to the liver; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                                                                                                                                                                                                                                                                                                                                GSM1228237

                                                                                                                                                                                                                                                                                                                                Uncertain

                                                                                                                                                                                                                                                                                                                                metastasized cancer AMC_24-3

                                                                                                                                                                                                                                                                                                                                Not included: the study role or selected requirements have incomplete or conflicting evidence. specimen category: Tissue or biopsy — Insufficient evidence. Study role: Case marker detected.

                                                                                                                                                                                                                                                                                                                                Requirements and decision evidence
                                                                                                                                                                                                                                                                                                                                • organism: Homo sapiens — Meets requirement
                                                                                                                                                                                                                                                                                                                                  • Supported by the indexed evidence.
                                                                                                                                                                                                                                                                                                                                  • organism_evidence_text: Homo sapiens
                                                                                                                                                                                                                                                                                                                                • assay type: bulk RNA-seq — Meets requirement
                                                                                                                                                                                                                                                                                                                                  • Supported by the indexed evidence.
                                                                                                                                                                                                                                                                                                                                  • assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed b...
                                                                                                                                                                                                                                                                                                                                • specimen category: Tissue or biopsy — Insufficient evidence
                                                                                                                                                                                                                                                                                                                                  • The required value is not reported.
                                                                                                                                                                                                                                                                                                                                  • excluded sample type excludes: cell line, organoid, xenograft — Meets requirement
                                                                                                                                                                                                                                                                                                                                    • Supported by the indexed evidence.
                                                                                                                                                                                                                                                                                                                                    • specimen category excludes: Biofluid — Meets requirement
                                                                                                                                                                                                                                                                                                                                      • Supported by the indexed evidence.
                                                                                                                                                                                                                                                                                                                                      Source metadata
                                                                                                                                                                                                                                                                                                                                      Source name
                                                                                                                                                                                                                                                                                                                                      metastasized cancer
                                                                                                                                                                                                                                                                                                                                      Characteristics
                                                                                                                                                                                                                                                                                                                                      tissue: metastatic colorectal cancer to the liver; ajcc stage: Stage IV
                                                                                                                                                                                                                                                                                                                                      Description
                                                                                                                                                                                                                                                                                                                                      Not reported
                                                                                                                                                                                                                                                                                                                                      Indexed organism evidence
                                                                                                                                                                                                                                                                                                                                      REPORTED · SAMPLE_REPORTED: Homo sapiens
                                                                                                                                                                                                                                                                                                                                      Indexed assay evidence
                                                                                                                                                                                                                                                                                                                                      MAPPED_FROM_REPORTED_TEXT · SAMPLE_MAPPED: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments
                                                                                                                                                                                                                                                                                                                                      Source
                                                                                                                                                                                                                                                                                                                                      GEO
                                                                                                                                                                                                                                                                                                                                      Original indexed metadata
                                                                                                                                                                                                                                                                                                                                      sample_accession: GSM1228237
sample_title: metastasized cancer AMC_24-3
source_name: metastasized cancer
characteristics: tissue: metastatic colorectal cancer to the liver; ajcc stage: Stage IV
description: 
organism_code: HOMO_SAPIENS
organism_evidence_status: REPORTED
organism_evidence_source: SAMPLE_REPORTED
organism_evidence_text: Homo sapiens
assay_type_code: BULK_RNA_SEQ
assay_evidence_status: MAPPED_FROM_REPORTED_TEXT
assay_evidence_source: SAMPLE_MAPPED
assay_evidence_text: Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.; Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.; Base calling was performed by Illumina Genome Studio(V2010.1).; A reference genome sequence data of Homo sapiens was obtained from University of California Santa Cruz (UCSC) Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).; To estimate average and standard deviation of fragment size of paired-end reads, reference transcriptome was generated by MakeTranscriptome component of USeq tool (ver. 8.4.4, http://useq.sourceforge.net/). Then, generated reference transcriptome was indexed by Novoindex followed by reads mapping to transcriptome and measurements of average and standard deviation of fragment size in paired-end reads using Novoalign provided by Novocraft software (ver. 2.8.3, http://www.novocraft.com/). Tophat2 was applied to tissue samples for mapping reads to reference genome and estimated average and standard deviation of fragment size of each sample were used as parameters of Tophat2.; The fragments 
per 
kilobase
 of 
transcript
 per 
million
 fragments 
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).; Genome_build: hg19; Supplementary_files_format_and_content: tab-delimited text format with FPFM values; RNA-Seq

                                                                                                                                                                                                                                                                                                                                      Excluded samples (0)

                                                                                                                                                                                                                                                                                                                                      No excluded samples.