GSE155301

Comprehensive transcriptome profiling of ulcerative colitis mouse model suggests biomarkers and therapeutic targets for human colitis [RNA-Seq]

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

6 case / 6 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
Mus musculus
Whole-study samples
12 samples
Specimen
Biofluid
Reported/interpreted study design
Disease/model vs control Design classification does not establish patient pairs.
Comparison type
Tumor vs normal
Contributors
Yarani R, Palasca O, Gorodkin J, Pociot F
Contact name
Reza Yarani
Submission date
2020-07-28
Last update
2023-08-22
Organization
Steno Diabetes Center Copenhagen
Department
Not available
Public date
2021-03-13
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL21103 Illumina HiSeq 4000 (Mus musculus)
Series type
SubSeries
SubSeries
Not available
BioProject
PRJNA649271

Summary

BACKGROUND & AIMS: Ulcerative colitis (UC) is an inflammatory bowel disorder with unknown etiology, and given its complex nature, an in vivo model to study its pathophysiology is vital. Animal models play an important role in molecular profiling necessary to pinpoint mechanisms that contribute to human disease. Thus, we aim to identify common conserved gene expression signatures and differentially regulated pathways between human UC and a mouse model hereof, which can be used to identify UC patients from healthy individuals and to suggest novel treatment targets and biomarker candidates. METHODS: Therefore, we performed high-throughput total and small RNA sequencing to comprehensively characterize the transcriptome landscape of the most widely used UC mouse model, the dextran sodium sulfate (DSS) model. We used this data in conjunction with publicly available human UC transcriptome data to compare gene expression profiles and pathways. RESULTS: We identified differentially regulated protein-coding genes, long non-coding RNAs and microRNAs from colon and whole blood of UC mice and further characterized the involved pathways and biological processes through which these genes may contribute to disease development and progression. By integrating human and mouse UC datasets, we suggest a set of 51 differentially regulated genes in UC colon and blood that may improve molecular phenotyping, as well as aid in treatment decisions, drug discovery and the design of clinical trials. CONCLUSION: Global transcriptome analysis of the DSS-UC mouse model supports its use as an efficient high-throughput tool to discover new targets for therapeutic and diagnostic applications in human UC through identifying relationships between gene expression and disease phenotype.

Overall design

Total RNA (minus small RNA) profiling of colon and blood of 3 dextran sulfate sodium mouse model of acute ulcerative colitis and 3 healthy controls

Source Evidence

4 sources
Source Contribution Status
GEO

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

Sample records
12 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

Publication context when PubMed identifiers are already known.

 No match found

Metadata Quality Components

Persisted metadata quality

100 pts
Clarity
100%
Weight
100 pts

Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. Group clarity: Rule-based grouping found both case and control samples. 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

Review before analysis
90% DE readiness

Contrast completeness

25/25 pts

Both case and control groups are present in the proposed grouping.

Minimum group size

20/20 pts

Each contrast group has at least 2 samples.

Processed data availability

20/20 pts

Processed data is marked available in the GEO index.

Sample decision clarity

15/15 pts

All samples are assigned to a case or control group.

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

  • Critical dataset warnings must be resolved.
  • Secondary RNA assay context should be analyzed separately from ordinary bulk RNA-seq.

Next Steps

  • Resolve critical warnings before downstream analysis.

Analysis Preparation Checklist

5/6 ready

Group labels reviewed

Needs review

Siftome proposed case and control labels, but no reviewer confirmation is stored yet.

Open the sample grouping CSV and confirm group labels before analysis.

Minimum sample count met

Ready

Both groups meet the minimum of 2 samples.

Confirm whether the cohort is large enough for the intended statistical analysis.

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

Ready

No review-needed or unassigned samples are present in the proposed grouping.

Review the grouping table for biologically meaningful differences that the automated checks may not detect.

Exclusion decisions recorded

Ready

No hard-excluded samples were detected by the current rules.

Record any manual exclusions in the downstream analysis notes.

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.

Critical dataset warnings are present.

Assay context may require expert handling before DESeq2-style 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

  • Organism differs from search intent Mus musculus Search intent expects Homo sapiens. Organism came from Normalization rules.
  • Disease context Inflammatory bowel disease, ulcerative colitis Disease context came from Normalization rules.
  • Likely case group Ulcerative colitis 6 samples
  • Likely control group Control 6 samples

Intent Interpretation

  • Downgrade or exclusion reason Downgraded for tissue search because it is a biofluid cohort. Derived from current-intent ranking reasons.

Ranking Facts

Supporting evidence

  • Comparison: Disease/model vs control. Specimen: Biofluid. Comparison suitability: 0%.
  • Prioritized assay: bulk RNA-seq is the active assay expectation.
  • Interpreted disease metadata: Inflammatory bowel disease, Ulcerative colitis.
  • Processed data is available for downstream review.

Cautions

  • Downgraded for tissue search because it is a biofluid cohort.
  • Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
  • Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
  • Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking.
  • Overall score capped because comparison suitability is weak for the selected search intent.
  • Overall score capped because non-human datasets are outside the selected human ranking intent.
  • Overall score capped because secondary RNA assays are not primary mRNA tissue RNA-seq.
  • Comparison suitability score is below the Phase 1 recommended threshold.

Dataset Warnings

Normalized Fields

49 fields

Sample Group Preview

12 rows shown Show Hide
Study totals: Case 6 | Control 6 | Unassigned 0 | Excluded 0 | Ambiguous 0 12 rows shown
Group Role Accession Title Source / characteristics Reason
Ulcerative colitis Case GSM4698731 M1-3 Colon Disease state: Ulcerative colitis; Tissue: BLOOD; Strain: C57BL/6 Case marker detected.
Ulcerative colitis Case GSM4698732 M2-3 Colon Disease state: Ulcerative colitis; Tissue: BLOOD; Strain: C57BL/6 Case marker detected.
Ulcerative colitis Case GSM4698733 M4-3 Colon Disease state: Ulcerative colitis; Tissue: BLOOD; Strain: C57BL/6 Case marker detected.
Ulcerative colitis Case GSM4698737 MC1 Blood Disease state: Ulcerative colitis; Tissue: COLON; Strain: C57BL/6 Case marker detected.
Ulcerative colitis Case GSM4698738 MC2 Blood Disease state: Ulcerative colitis; Tissue: COLON; Strain: C57BL/6 Case marker detected.
Ulcerative colitis Case GSM4698739 MC4 Blood Disease state: Ulcerative colitis; Tissue: COLON; Strain: C57BL/6 Case marker detected.
Control Control GSM4698734 M7-3 Colon Disease state: Control; Tissue: BLOOD; Strain: C57BL/6 Sample-local control marker detected.
Control Control GSM4698735 M8-3 Colon Disease state: Control; Tissue: BLOOD; Strain: C57BL/6 Sample-local control marker detected.
Control Control GSM4698736 M9-3 Colon Disease state: Control; Tissue: BLOOD; Strain: C57BL/6 Sample-local control marker detected.
Control Control GSM4698740 MC7 Blood Disease state: Control; Tissue: COLON; Strain: C57BL/6 Sample-local control marker detected.
Control Control GSM4698741 MC8 Blood Disease state: Control; Tissue: COLON; Strain: C57BL/6 Sample-local control marker detected.
Control Control GSM4698742 MC9 Blood Disease state: Control; Tissue: COLON; Strain: C57BL/6 Sample-local control marker detected.

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.