GSE228122

Bulk RNA-seq of whole biopsies and enteroids/colonoids from terminal ileum and rectum of inflammatory bowel disease patients or control subjects

Whole-study status Not suitable

Dataset does not meet the current suitability threshold.

Whole-study downloads — these do not apply your sample requirements.

Selected cohort requirements

Samples meeting selected requirements: 0 cases / 0 controls

View matching samples

28 case / 0 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.

Source
GEO
Assay
bulk RNA-seq
Organism
Homo sapiens
Whole-study samples
115 samples
Specimen
Biopsy
Reported/interpreted study design
Unclear study design Design classification does not establish patient pairs.
Comparison type
Tumor vs normal
Contributors
Hamilton KE, Karakasheva T, Zhou Y
Contact name
Yusen Zhou
Submission date
2023-03-24
Last update
2023-09-27
Organization
Children's hospital of Philadelphia
Department
Department of Biomedical and Health Informatics
Public date
2023-08-22
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
PRJNA948350

Summary

The study was design to compare transcriptomic profiles of whole biopsies to enteroid/colonoid lines derived from them. In the accompanying publication, we observed substantial overlap of pathways upregulated in Crohn’s disease in enteroids and ileal biopsies, as well as colonoids and rectal biopsies. Our data support the use of patient enteroids and colonoids as critical translational tools for the study of inflammatory bowel disease.

Overall design

The biopsies were subjected to RNA extraction (Trizol) whole and subsequent library preparation and RNA-seq. To establish enteroids and colonoids, we first isolated crypts from matching biopsies, then seeded these crypts in Matrigel domes. We used complete human IntestiCult OGM to enteroid/colonoid growth. The cultures were passaged once, and then harvested for RNA isolation, library prep and RNA-seq.

Source Evidence

4 sources
Source Contribution Status
GEO

Original dataset metadata, sample metadata, source links, and GEO data availability flags.

Sample records
115 GSM samples
 Primary source
recount3

Planned trusted source for processed count availability.

 No match found
Expression Atlas

Planned source for curated expression experiment links.

 No match found
PubMed

Primary GEO citations and related PubMed articles that mention this dataset.

1 linked publication 1 DOI

Primary publication

  1. Patient-derived Colonoids From Disease-spared Tissue Retain Inflammatory Bowel Disease-specific Transcriptomic Signatures. Gastro hep advances, 2023
Available

Metadata Quality Components

Persisted metadata quality

93 pts
Clarity
93%
Weight
100 pts

Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. Group clarity: Only one side of the comparison is clearly grouped. Disease clarity: Disease or condition metadata normalized. Tissue clarity: Anatomical source metadata normalized. Treatment clarity: No unclear treatment split detected in the sample metadata. Replicate clarity: No pooled sample or technical replicate flags detected. Data availability clarity: Dataset-level processed or raw data availability is explicit.

Analysis Readiness

Not ready
43% DE readiness

Contrast completeness

10/25 pts

Only one side of the contrast is present; downstream DE needs both groups.

Minimum group size

0/20 pts

Minimum group size cannot be evaluated until a complete contrast exists.

Processed data availability

20/20 pts

Processed data is marked available in the GEO index.

Sample decision clarity

3/15 pts

Unassigned or review-needed samples remain before analysis.

Blocking warnings

0/10 pts

Critical warnings must be resolved before downstream analysis.

Metadata normalization

10/10 pts

Metadata quality is high enough to support downstream handoff.

Blockers

  • No complete case/control contrast is available.
  • 30 samples are still unassigned.
  • 1 samples need manual grouping review.
  • Critical dataset warnings must be resolved.

Next Steps

  • Resolve unassigned or review-needed samples in the grouping table.
  • Confirm excluded samples before creating the final analysis metadata file.
  • Resolve critical warnings before downstream analysis.

Analysis Preparation Checklist

2/6 ready

Group labels reviewed

Blocked

No complete case/control grouping exists yet.

Review the sample grouping table and assign both case and control groups.

Minimum sample count met

Blocked

At least one group has fewer than 2 samples.

Choose a larger dataset or merge only scientifically valid groups.

Processed counts available

Ready

Processed data availability is marked true in the GEO index.

Verify that downloaded processed files contain usable count or expression identifiers.

Ambiguous samples handled

Needs review

1 review-needed samples and 30 unassigned samples remain.

Resolve ambiguous and unassigned samples before finalizing the contrast.

Exclusion decisions recorded

Needs review

57 samples have hard exclusion flags in the proposed grouping.

Confirm excluded samples and preserve the reason in the analysis handoff.

Source traceability preserved

Ready

The dataset and sample accessions can be traced back to GEO.

Keep GEO accessions with exported metadata.

Bioinformatician Review

Bioinformatician review required

Ask a bioinformatician to review grouping, count availability, exclusions, and design before DE.

Analysis readiness has blockers that must be resolved before DE.

Analysis preparation checklist contains blocked items.

No complete case/control or treatment/control contrast is available.

At least one comparison group has fewer than two samples.

One or more samples are unassigned and need manual grouping decisions.

One or more samples were flagged for manual review.

Critical dataset warnings are present.

Study design is model-system or unclear and should be reviewed before analysis.

Why This Is Ranked Here

Tumor vs normal
Not suitable Dataset does not meet the current suitability threshold.

Applied Review Decisions

No active review decisions affect this ranking.

Derived Classifications

  • Disease context Crohn's disease, inflammatory bowel disease, ulcerative colitis Disease context came from Normalization rules.
  • Likely case group Inflammatory bowel disease 28 samples
  • Likely control group No control group detected 0 samples

Intent Interpretation

  • Downgrade or exclusion reason Comparison: Unclear study design. Specimen: Biopsy. Comparison suitability: 0%. Derived from current-intent ranking reasons.

Ranking Facts

Supporting evidence

  • Prioritized assay: bulk RNA-seq is the active assay expectation.
  • Interpreted disease metadata: Crohn's disease, Inflammatory bowel disease, Ulcerative colitis.
  • Processed data is available for downstream review.
  • External evidence: PubMed links 1 publication; 1 DOI available: PMID 37736163.
  • Publication context: Patient-derived Colonoids From Disease-spared Tissue Retain Inflammatory Bowel Disease-specific Transcriptomic Signatures.. Gastro hep advances, 2023. PMID 37736163. DOI 10.1016/j.gastha.2023.05.003.

Cautions

  • Comparison: Unclear study design. Specimen: Biopsy. Comparison suitability: 0%.
  • Downgraded for tissue search because study design or specimen source is unclear.
  • Excluded sample type flags reduce suitability.
  • Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
  • Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
  • Excluded model-system sample markers reduce suitability.
  • Overall score capped because comparison suitability is weak for the selected search intent.
  • Missing or unclear metadata. Comparison - Unclear study design. Specimen - Biopsy. Comparison suitability: 0%.
  • Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
  • Comparison suitability score is below the Phase 1 recommended threshold.

Dataset Warnings

Normalized Fields

487 fields

Sample Group Preview

showing 108 of 115 preview rows Show Hide
Study totals: Case 28 | Control 0 | Unassigned 30 | Excluded 57 | Ambiguous 0 showing 108 of 115 preview rows
Group Role Accession Title Source / characteristics Reason
Inflammatory bowel disease Case GSM7114707 Biopsy data from sample 1375752274 Ileum Tissue: Ileum; Cell type: Biopsy; Disease state: IBD; Diagnosis: CD Case marker detected.
Inflammatory bowel disease Case GSM7114708 Biopsy data from sample 1643751206 Rectum Tissue: Rectum; Cell type: Biopsy; Disease state: IBD; Diagnosis: IBDU Case marker detected.
Inflammatory bowel disease Case GSM7114711 Biopsy data from sample 2071726996 Ileum Tissue: Ileum; Cell type: Biopsy; Disease state: IBD; Diagnosis: CD Case marker detected.
Inflammatory bowel disease Case GSM7114713 Biopsy data from sample 2356159714 Rectum Tissue: Rectum; Cell type: Biopsy; Disease state: IBD; Diagnosis: IBDU Case marker detected.
Ulcerative colitis Case GSM7114714 Biopsy data from sample 2426597717 Ileum Tissue: Ileum; Cell type: Biopsy; Disease state: IBD; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM7114715 Biopsy data from sample 2646146994 Rectum Tissue: Rectum; Cell type: Biopsy; Disease state: IBD; Diagnosis: UC Case marker detected.
Inflammatory bowel disease Case GSM7114716 Biopsy data from sample 2848225596 Ileum Tissue: Ileum; Cell type: Biopsy; Disease state: IBD; Diagnosis: IBDU Case marker detected.
Inflammatory bowel disease Case GSM7114717 Biopsy data from sample 3028669805 Ileum Tissue: Ileum; Cell type: Biopsy; Disease state: IBD; Diagnosis: CD Case marker detected.
Inflammatory bowel disease Case GSM7114719 Biopsy data from sample 3269365601 Rectum Tissue: Rectum; Cell type: Biopsy; Disease state: IBD; Diagnosis: CD Case marker detected.
Inflammatory bowel disease Case GSM7114720 Biopsy data from sample 3312689543 Rectum Tissue: Rectum; Cell type: Biopsy; Disease state: IBD; Diagnosis: CD Case marker detected.
Inflammatory bowel disease Case GSM7114725 Biopsy data from sample 3684376931 Ileum Tissue: Ileum; Cell type: Biopsy; Disease state: IBD; Diagnosis: IBDU Case marker detected.
Ulcerative colitis Case GSM7114728 Biopsy data from sample 3943331569 Rectum Tissue: Rectum; Cell type: Biopsy; Disease state: IBD; Diagnosis: UC Case marker detected.
Inflammatory bowel disease Case GSM7114729 Biopsy data from sample 4001235543 Ileum Tissue: Ileum; Cell type: Biopsy; Disease state: IBD; Diagnosis: IBDU Case marker detected.
Inflammatory bowel disease Case GSM7114731 Biopsy data from sample 4181037523 Ileum Tissue: Ileum; Cell type: Biopsy; Disease state: IBD; Diagnosis: CD Case marker detected.
Inflammatory bowel disease Case GSM7114734 Biopsy data from sample 4379496952 Rectum Tissue: Rectum; Cell type: Biopsy; Disease state: IBD; Diagnosis: IcCD Case marker detected.
Ulcerative colitis Case GSM7114735 Biopsy data from sample 4538991461 Ileum Tissue: Ileum; Cell type: Biopsy; Disease state: IBD; Diagnosis: UC Case marker detected.
Inflammatory bowel disease Case GSM7114736 Biopsy data from sample 5395385401 Ileum Tissue: Ileum; Cell type: Biopsy; Disease state: IBD; Diagnosis: CD Case marker detected.
Ulcerative colitis Case GSM7114739 Biopsy data from sample 6195746358 Rectum Tissue: Rectum; Cell type: Biopsy; Disease state: IBD; Diagnosis: UC Case marker detected.
Inflammatory bowel disease Case GSM7114743 Biopsy data from sample 6662556960 Rectum Tissue: Rectum; Cell type: Biopsy; Disease state: IBD; Diagnosis: CD Case marker detected.
Inflammatory bowel disease Case GSM7114744 Biopsy data from sample 6733092745 Ileum Tissue: Ileum; Cell type: Biopsy; Disease state: IBD; Diagnosis: IcCD Case marker detected.
Ulcerative colitis Case GSM7114746 Biopsy data from sample 6838739690 Rectum Tissue: Rectum; Cell type: Biopsy; Disease state: IBD; Diagnosis: UC Case marker detected.
Inflammatory bowel disease Case GSM7114747 Biopsy data from sample 7051356862 Rectum Tissue: Rectum; Cell type: Biopsy; Disease state: IBD; Diagnosis: CD Case marker detected.
Inflammatory bowel disease Case GSM7114750 Biopsy data from sample 7214955558 Rectum Tissue: Rectum; Cell type: Biopsy; Disease state: IBD; Diagnosis: IBDU Case marker detected.
Inflammatory bowel disease Case GSM7114754 Biopsy data from sample 8672611246 Rectum Tissue: Rectum; Cell type: Biopsy; Disease state: IBD; Diagnosis: CD Case marker detected.
Inflammatory bowel disease Case GSM7114755 Biopsy data from sample 8766675562 Rectum Tissue: Rectum; Cell type: Biopsy; Disease state: IBD; Diagnosis: CD Case marker detected.
Ulcerative colitis Case GSM7114757 Biopsy data from sample 9096494786 Ileum Tissue: Ileum; Cell type: Biopsy; Disease state: IBD; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM7114760 Biopsy data from sample 9695702256 Rectum Tissue: Rectum; Cell type: Biopsy; Disease state: IBD; Diagnosis: UC Case marker detected.
Ulcerative colitis Case GSM7114763 Biopsy data from sample 9971793399 Ileum Tissue: Ileum; Cell type: Biopsy; Disease state: IBD; Diagnosis: UC Case marker detected.
Unassigned Unassigned GSM7114706 Biopsy data from sample 1204719929 Rectum Tissue: Rectum; Cell type: Biopsy; Disease state: NPD; Diagnosis: CTR No explicit case or control marker detected.
Unassigned Unassigned GSM7114709 Biopsy data from sample 1737224884 Rectum Tissue: Rectum; Cell type: Biopsy; Disease state: NPD; Diagnosis: CTR No explicit case or control marker detected.
Unassigned Unassigned GSM7114710 Biopsy data from sample 1878769109 Rectum Tissue: Rectum; Cell type: Biopsy; Disease state: NPD; Diagnosis: CTR No explicit case or control marker detected.
Unassigned Unassigned GSM7114712 Biopsy data from sample 2087695933 Ileum Tissue: Ileum; Cell type: Biopsy; Disease state: NPD; Diagnosis: CTR No explicit case or control marker detected.
Unassigned Unassigned GSM7114718 Biopsy data from sample 3179088571 Ileum Tissue: Ileum; Cell type: Biopsy; Disease state: NPD; Diagnosis: CTR No explicit case or control marker detected.
Unassigned Unassigned GSM7114721 Biopsy data from sample 3359263969 Rectum Tissue: Rectum; Cell type: Biopsy; Disease state: NPD; Diagnosis: CTR No explicit case or control marker detected.
Unassigned Unassigned GSM7114722 Biopsy data from sample 3552931053 Rectum Tissue: Rectum; Cell type: Biopsy; Disease state: NPD; Diagnosis: CTR No explicit case or control marker detected.
Unassigned Unassigned GSM7114723 Biopsy data from sample 3553318929 Rectum Tissue: Rectum; Cell type: Biopsy; Disease state: NPD; Diagnosis: CTR No explicit case or control marker detected.
Unassigned Unassigned GSM7114724 Biopsy data from sample 3631280583 Ileum Tissue: Ileum; Cell type: Biopsy; Disease state: NPD; Diagnosis: CTR No explicit case or control marker detected.
Unassigned Unassigned GSM7114726 Biopsy data from sample 3723636182 Ileum Tissue: Ileum; Cell type: Biopsy; Disease state: NPD; Diagnosis: CTR No explicit case or control marker detected.
Unassigned Unassigned GSM7114727 Biopsy data from sample 3818749482 Ileum Tissue: Ileum; Cell type: Biopsy; Disease state: NPD; Diagnosis: CTR No explicit case or control marker detected.
Unassigned Unassigned GSM7114730 Biopsy data from sample 4028176603 Ileum Tissue: Ileum; Cell type: Biopsy; Disease state: NPD; Diagnosis: CTR No explicit case or control marker detected.
Unassigned Unassigned GSM7114732 Biopsy data from sample 4291720641 Ileum Tissue: Ileum; Cell type: Biopsy; Disease state: NPD; Diagnosis: CTR No explicit case or control marker detected.
Unassigned Unassigned GSM7114733 Biopsy data from sample 4304050535 Rectum Tissue: Rectum; Cell type: Biopsy; Disease state: NPD; Diagnosis: CTR No explicit case or control marker detected.
Unassigned Unassigned GSM7114737 Biopsy data from sample 5792732371 Ileum Tissue: Ileum; Cell type: Biopsy; Disease state: NPD; Diagnosis: CTR No explicit case or control marker detected.
Unassigned Unassigned GSM7114738 Biopsy data from sample 5939318740 Ileum Tissue: Ileum; Cell type: Biopsy; Disease state: NPD; Diagnosis: CTR No explicit case or control marker detected.
Unassigned Unassigned GSM7114740 Biopsy data from sample 6332115407 Ileum Tissue: Ileum; Cell type: Biopsy; Disease state: NPD; Diagnosis: CTR No explicit case or control marker detected.
Unassigned Unassigned GSM7114741 Biopsy data from sample 6421694263 Ileum Tissue: Ileum; Cell type: Biopsy; Disease state: NPD; Diagnosis: CTR No explicit case or control marker detected.
Unassigned Unassigned GSM7114742 Biopsy data from sample 6445622918 Rectum Tissue: Rectum; Cell type: Biopsy; Disease state: NPD; Diagnosis: CTR No explicit case or control marker detected.
Unassigned Unassigned GSM7114745 Biopsy data from sample 6739821734 Rectum Tissue: Rectum; Cell type: Biopsy; Disease state: NPD; Diagnosis: CTR No explicit case or control marker detected.
Unassigned Unassigned GSM7114748 Biopsy data from sample 7139077478 Ileum Tissue: Ileum; Cell type: Biopsy; Disease state: NPD; Diagnosis: CTR No explicit case or control marker detected.
Unassigned Unassigned GSM7114749 Biopsy data from sample 7143294781 Rectum Tissue: Rectum; Cell type: Biopsy; Disease state: NPD; Diagnosis: CTR No explicit case or control marker detected.
Unassigned Unassigned GSM7114751 Biopsy data from sample 7800901725 Rectum Tissue: Rectum; Cell type: Biopsy; Disease state: NPD; Diagnosis: CTR No explicit case or control marker detected.
Unassigned Unassigned GSM7114752 Biopsy data from sample 7807216273 Ileum Tissue: Ileum; Cell type: Biopsy; Disease state: NPD; Diagnosis: CTR No explicit case or control marker detected.
Unassigned Unassigned GSM7114753 Biopsy data from sample 8081214457 Rectum Tissue: Rectum; Cell type: Biopsy; Disease state: NPD; Diagnosis: CTR No explicit case or control marker detected.
Unassigned Unassigned GSM7114756 Biopsy data from sample 8986797186 Rectum Tissue: Rectum; Cell type: Biopsy; Disease state: NPD; Diagnosis: CTR No explicit case or control marker detected.
Unassigned Unassigned GSM7114758 Biopsy data from sample 9325947159 Rectum Tissue: Rectum; Cell type: Biopsy; Disease state: NPD; Diagnosis: CTR No explicit case or control marker detected.
Unassigned Unassigned GSM7114759 Biopsy data from sample 9433080982 Rectum Tissue: Rectum; Cell type: Biopsy; Disease state: NPD; Diagnosis: CTR No explicit case or control marker detected.
Unassigned Unassigned GSM7114761 Biopsy data from sample 9823004282 Ileum Tissue: Ileum; Cell type: Biopsy; Disease state: NPD; Diagnosis: CTR No explicit case or control marker detected.
Unassigned Unassigned GSM7114762 Biopsy data from sample 9940753211 Ileum Tissue: Ileum; Cell type: Biopsy; Disease state: NPD; Diagnosis: CTR No explicit case or control marker detected.
Excluded: Organoid Excluded GSM7114764 Organoid data from sample 40002596246 Ileum Tissue: Ileum; Cell type: Organoid; Disease state: NPD; Diagnosis: CTR organoid: Normalized exclusion flag detected: organoid.
Excluded: Organoid Excluded GSM7114765 Organoid data from sample 40021655987 Rectum Tissue: Rectum; Cell type: Organoid; Disease state: IBD; Diagnosis: UC organoid: Normalized exclusion flag detected: organoid.
Excluded: Organoid Excluded GSM7114766 Organoid data from sample 40066983148 Ileum Tissue: Ileum; Cell type: Organoid; Disease state: NPD; Diagnosis: CTR organoid: Normalized exclusion flag detected: organoid.
Excluded: Organoid Excluded GSM7114767 Organoid data from sample 40085042880 Ileum Tissue: Ileum; Cell type: Organoid; Disease state: NPD; Diagnosis: CTR organoid: Normalized exclusion flag detected: organoid.
Excluded: Organoid Excluded GSM7114768 Organoid data from sample 40103927684 Ileum Tissue: Ileum; Cell type: Organoid; Disease state: IBD; Diagnosis: UC organoid: Normalized exclusion flag detected: organoid.
Excluded: Organoid Excluded GSM7114769 Organoid data from sample 40120371040 Rectum Tissue: Rectum; Cell type: Organoid; Disease state: NPD; Diagnosis: CTR organoid: Normalized exclusion flag detected: organoid.
Excluded: Organoid Excluded GSM7114770 Organoid data from sample 40149430782 Rectum Tissue: Rectum; Cell type: Organoid; Disease state: IBD; Diagnosis: IcCD organoid: Normalized exclusion flag detected: organoid.
Excluded: Organoid Excluded GSM7114771 Organoid data from sample 40167315587 Ileum Tissue: Ileum; Cell type: Organoid; Disease state: IBD; Diagnosis: CD organoid: Normalized exclusion flag detected: organoid.
Excluded: Organoid Excluded GSM7114772 Organoid data from sample 40184868943 Rectum Tissue: Rectum; Cell type: Organoid; Disease state: IBD; Diagnosis: IBDU organoid: Normalized exclusion flag detected: organoid.
Excluded: Organoid Excluded GSM7114773 Organoid data from sample 40187474238 Rectum Tissue: Rectum; Cell type: Organoid; Disease state: NA; Diagnosis: IcCD organoid: Normalized exclusion flag detected: organoid.; ambiguous sample: Ambiguous case/control metadata detected.
Excluded: Organoid Excluded GSM7114774 Organoid data from sample 40205268033 Rectum Tissue: Rectum; Cell type: Organoid; Disease state: NPD; Diagnosis: CTR organoid: Normalized exclusion flag detected: organoid.
Excluded: Organoid Excluded GSM7114775 Organoid data from sample 40221702489 Rectum Tissue: Rectum; Cell type: Organoid; Disease state: IBD; Diagnosis: IBDU organoid: Normalized exclusion flag detected: organoid.
Excluded: Organoid Excluded GSM7114776 Organoid data from sample 40238256845 Ileum Tissue: Ileum; Cell type: Organoid; Disease state: NPD; Diagnosis: CTR organoid: Normalized exclusion flag detected: organoid.
Excluded: Organoid Excluded GSM7114777 Organoid data from sample 40241871131 Rectum Tissue: Rectum; Cell type: Organoid; Disease state: NPD; Diagnosis: CTR organoid: Normalized exclusion flag detected: organoid.
Excluded: Organoid Excluded GSM7114778 Organoid data from sample 40256130640 Rectum Tissue: Rectum; Cell type: Organoid; Disease state: NPD; Diagnosis: CTR organoid: Normalized exclusion flag detected: organoid.
Excluded: Organoid Excluded GSM7114779 Organoid data from sample 40285199382 Rectum Tissue: Rectum; Cell type: Organoid; Disease state: IBD; Diagnosis: CD organoid: Normalized exclusion flag detected: organoid.
Excluded: Organoid Excluded GSM7114780 Organoid data from sample 40292643748 Rectum Tissue: Rectum; Cell type: Organoid; Disease state: NPD; Diagnosis: CTR organoid: Normalized exclusion flag detected: organoid.
Excluded: Organoid Excluded GSM7114781 Organoid data from sample 40310528543 Rectum Tissue: Rectum; Cell type: Organoid; Disease state: NPD; Diagnosis: CTR organoid: Normalized exclusion flag detected: organoid.
Excluded: Organoid Excluded GSM7114782 Organoid data from sample 40323143838 Rectum Tissue: Rectum; Cell type: Organoid; Disease state: IBD; Diagnosis: UC organoid: Normalized exclusion flag detected: organoid.
Excluded: Organoid Excluded GSM7114783 Organoid data from sample 40349687284 Rectum Tissue: Rectum; Cell type: Organoid; Disease state: NPD; Diagnosis: CTR organoid: Normalized exclusion flag detected: organoid.
Excluded: Organoid Excluded GSM7114784 Organoid data from sample 40369756936 Rectum Tissue: Rectum; Cell type: Organoid; Disease state: IBD; Diagnosis: UC organoid: Normalized exclusion flag detected: organoid.
Excluded: Organoid Excluded GSM7114785 Organoid data from sample 40374915445 Ileum Tissue: Ileum; Cell type: Organoid; Disease state: IBD; Diagnosis: UC organoid: Normalized exclusion flag detected: organoid.
Excluded: Organoid Excluded GSM7114786 Organoid data from sample 40393074187 Ileum Tissue: Ileum; Cell type: Organoid; Disease state: NPD; Diagnosis: CTR organoid: Normalized exclusion flag detected: organoid.
Excluded: Organoid Excluded GSM7114787 Organoid data from sample 40404416536 Ileum Tissue: Ileum; Cell type: Organoid; Disease state: NPD; Diagnosis: CTR organoid: Normalized exclusion flag detected: organoid.
Excluded: Organoid Excluded GSM7114788 Organoid data from sample 40411969992 Rectum Tissue: Rectum; Cell type: Organoid; Disease state: NPD; Diagnosis: CTR organoid: Normalized exclusion flag detected: organoid.
Excluded: Organoid Excluded GSM7114789 Organoid data from sample 40438303348 Rectum Tissue: Rectum; Cell type: Organoid; Disease state: NPD; Diagnosis: CTR organoid: Normalized exclusion flag detected: organoid.
Excluded: Organoid Excluded GSM7114790 Organoid data from sample 40440928633 Rectum Tissue: Rectum; Cell type: Organoid; Disease state: NPD; Diagnosis: CTR organoid: Normalized exclusion flag detected: organoid.
Excluded: Organoid Excluded GSM7114791 Organoid data from sample 40457462089 Rectum Tissue: Rectum; Cell type: Organoid; Disease state: IBD; Diagnosis: UC organoid: Normalized exclusion flag detected: organoid.
Excluded: Organoid Excluded GSM7114792 Organoid data from sample 40486531731 Ileum Tissue: Ileum; Cell type: Organoid; Disease state: IBD; Diagnosis: CD organoid: Normalized exclusion flag detected: organoid.
Excluded: Organoid Excluded GSM7114793 Organoid data from sample 40512291331 Ileum Tissue: Ileum; Cell type: Organoid; Disease state: IBD; Diagnosis: IcCD organoid: Normalized exclusion flag detected: organoid.
Excluded: Organoid Excluded GSM7114794 Organoid data from sample 40539744797 Ileum Tissue: Ileum; Cell type: Organoid; Disease state: IBD; Diagnosis: UC organoid: Normalized exclusion flag detected: organoid.
Excluded: Organoid Excluded GSM7114795 Organoid data from sample 40558803438 Ileum Tissue: Ileum; Cell type: Organoid; Disease state: NPD; Diagnosis: CTR organoid: Normalized exclusion flag detected: organoid.
Excluded: Organoid Excluded GSM7114796 Organoid data from sample 40575357894 Ileum Tissue: Ileum; Cell type: Organoid; Disease state: IBD; Diagnosis: IBDU organoid: Normalized exclusion flag detected: organoid.
Excluded: Organoid Excluded GSM7114797 Organoid data from sample 40593132699 Ileum Tissue: Ileum; Cell type: Organoid; Disease state: IBD; Diagnosis: UC organoid: Normalized exclusion flag detected: organoid.
Excluded: Organoid Excluded GSM7114798 Organoid data from sample 40611017494 Ileum Tissue: Ileum; Cell type: Organoid; Disease state: IBD; Diagnosis: CD organoid: Normalized exclusion flag detected: organoid.
Excluded: Organoid Excluded GSM7114799 Organoid data from sample 40614622780 Rectum Tissue: Rectum; Cell type: Organoid; Disease state: IBD; Diagnosis: IBDU organoid: Normalized exclusion flag detected: organoid.
Excluded: Organoid Excluded GSM7114800 Organoid data from sample 40630176136 Rectum Tissue: Rectum; Cell type: Organoid; Disease state: IBD; Diagnosis: UC organoid: Normalized exclusion flag detected: organoid.
Excluded: Organoid Excluded GSM7114801 Organoid data from sample 40657629592 Rectum Tissue: Rectum; Cell type: Organoid; Disease state: IBD; Diagnosis: CD organoid: Normalized exclusion flag detected: organoid.
Excluded: Organoid Excluded GSM7114802 Organoid data from sample 40676788233 Rectum Tissue: Rectum; Cell type: Organoid; Disease state: IBD; Diagnosis: CD organoid: Normalized exclusion flag detected: organoid.
Excluded: Organoid Excluded GSM7114803 Organoid data from sample 40729892299 Rectum Tissue: Rectum; Cell type: Organoid; Disease state: IBD; Diagnosis: UC organoid: Normalized exclusion flag detected: organoid.
Excluded: Organoid Excluded GSM7114804 Organoid data from sample 40732507585 Rectum Tissue: Rectum; Cell type: Organoid; Disease state: NPD; Diagnosis: CTR organoid: Normalized exclusion flag detected: organoid.
Excluded: Organoid Excluded GSM7114805 Organoid data from sample 40758951931 Rectum Tissue: Rectum; Cell type: Organoid; Disease state: NPD; Diagnosis: CTR organoid: Normalized exclusion flag detected: organoid.
Excluded: Organoid Excluded GSM7114806 Organoid data from sample 40765404397 Rectum Tissue: Rectum; Cell type: Organoid; Disease state: NPD; Diagnosis: CTR organoid: Normalized exclusion flag detected: organoid.
Excluded: Organoid Excluded GSM7114807 Organoid data from sample 40778010682 Ileum Tissue: Ileum; Cell type: Organoid; Disease state: NPD; Diagnosis: CTR organoid: Normalized exclusion flag detected: organoid.
Excluded: Organoid Excluded GSM7114808 Organoid data from sample 40794563038 Ileum Tissue: Ileum; Cell type: Organoid; Disease state: NPD; Diagnosis: CTR organoid: Normalized exclusion flag detected: organoid.
Excluded: Organoid Excluded GSM7114809 Organoid data from sample 40812448833 Ileum Tissue: Ileum; Cell type: Organoid; Disease state: IBD; Diagnosis: IBDU organoid: Normalized exclusion flag detected: organoid.
Excluded: Organoid Excluded GSM7114810 Organoid data from sample 40820223638 Rectum Tissue: Rectum; Cell type: Organoid; Disease state: IBD; Diagnosis: CD organoid: Normalized exclusion flag detected: organoid.
Excluded: Organoid Excluded GSM7114811 Organoid data from sample 40847777094 Rectum Tissue: Rectum; Cell type: Organoid; Disease state: IBD; Diagnosis: UC organoid: Normalized exclusion flag detected: organoid.
Excluded: Organoid Excluded GSM7114812 Organoid data from sample 40859382280 Ileum Tissue: Ileum; Cell type: Organoid; Disease state: NPD; Diagnosis: CTR organoid: Normalized exclusion flag detected: organoid.
Excluded: Organoid Excluded GSM7114813 Organoid data from sample 40866836736 Ileum Tissue: Ileum; Cell type: Organoid; Disease state: IBD; Diagnosis: CD organoid: Normalized exclusion flag detected: organoid.
7 additional excluded samples are hidden from this preview.

Use as Discovery Cohort

External Validation Finder

Carry Siftome's disease, organism, specimen, assay, data type, and accession into a validation project. Uncertain fields remain Unknown.