GSE111889

Longitudinal Multi’omics of the Human Microbiome in Inflammatory Bowel Disease

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

250 case / 1 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
251 samples
Specimen
Biopsy
Reported/interpreted study design
Disease/model vs control Design classification does not establish patient pairs.
Comparison type
Tumor vs normal
Contributors
Arze C, Plichata D, Bishai J, Huttenhower C
Contact name
Curtis Huttenhower
Submission date
2018-03-15
Last update
2019-06-04
Organization
Harvard T.H. Chan School of Public Health
Department
Biostatistics
Public date
2018-03-17
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
PRJNA438663

Summary

Purpose: The main Inflammatory Bowel Disease (IBD) Multi'omics Database (IBDMDB) study includes multi’omics measurements from over 100 subjects, sampled biweekly over up to a year in both adult and pediatric patients with IBD (Crohn’s disease and ulcerative colitis), along with non-IBD controls. Data types include fecal metagenomes, metatranscriptomes, metabolomes, and proteomes, as well as host genetics, intestinal biopsy transcriptomes, epigenetics, and 16S amplicon profiles. Subjects’ medical histories and demographics are collected at baseline and medication, diet, and disease activity profiled longitudinally.  Methods: Methods: Total RNA was quantified using theQuant-iT™​ RiboGreen® RNA Assay Kit and normalized to 5ng/ul. Following plating, 2 uL of ERCC controls (using a 1:1000 dilution) were spiked into each sample. An aliquot of 200ng for each sample was transferred into library preparation which was an automated variant of​ ​the Illumina TruSeq™​ Stranded mRNA Sample Preparation Kit. This method preserves strand orientation of the RNA transcript. It uses oligo dT beads to select mRNA from the total RNA sample. It is followed by heat fragmentation and cDNA synthesis from the RNA template. The resultant 500bp cDNA then goes through library preparation (end repair, base ‘A’ addition, adapter ligation, and enrichment) using Broad designed indexed adapters substituted in for multiplexing. After enrichment the libraries were quantified using Quant-iT PicoGreen (1:200 dilution). After normalizing samples to 5 ng/uL, the set was pooled and quantified using the KAPA Library Quantification Kit for Illumina Sequencing Platforms. The entire process is in 96-well format and all pipetting is done by either Agilent Bravo or Hamilton Starlet. Pooled libraries were normalized to 2nM and denatured using 0.1 N NaOH prior to sequencing. Flowcell cluster amplification and sequencing were performed according to the manufacturer’s protocols using either the HiSeq 2000.

Overall design

RNA-seq analysis of biopsy samples retrieved from CD, UC and non-IBD patients enrolled in the HMP2 project. NOTE: Submitter declares that the raw data will be submitted to dbGaP (https://www.ncbi.nlm.nih.gov/gap) because of patient privacy concerns.

Source Evidence

4 sources
Source Contribution Status
GEO

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

Sample records
251 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.

3 linked publications 3 DOIs

Primary publication

  1. Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature, 2019

Related publications

  1. Neutrophil Infiltration Characterized by Upregulation of S100A8, S100A9, S100A12 and CXCR2 Is Associated With the Co-Occurrence of Crohn's Disease and Peripheral Artery Disease. Frontiers in immunology, 2022
  2. Microbial genetic and transcriptional contributions to oxalate degradation by the gut microbiota in health and disease. eLife, 2021
Available

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
85% DE readiness

Contrast completeness

25/25 pts

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

Minimum group size

8/20 pts

A contrast exists, but at least one group is below the minimum sample count.

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

7/10 pts

Warnings are present, but none are critical blockers.

Metadata normalization

10/10 pts

Metadata quality is high enough to support downstream handoff.

Blockers

  • At least one contrast group is below the minimum sample count.

Next Steps

  • Review blockers and update sample grouping or dataset selection before analysis.

Analysis Preparation Checklist

4/6 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

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

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.

Analysis preparation checklist contains blocked items.

At least one comparison group has fewer than two samples.

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 Crohn's disease 250 samples
  • Likely control group Non-inflamed tissue 1 samples

Ranking Facts

Supporting evidence

  • Comparison: Disease/model vs control. Specimen: Biopsy. Comparison suitability: 0%.
  • 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 3 publications; 3 DOIs available: PMID 31142855, PMID 33769280, PMID 35795659.
  • Publication context: Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases.. Nature, 2019. PMID 31142855. DOI 10.1038/s41586-019-1237-9.
  • Publication context: Microbial genetic and transcriptional contributions to oxalate degradation by the gut microbiota in health and disease.. eLife, 2021. PMID 33769280. DOI 10.7554/eLife.63642.
  • Publication context: Neutrophil Infiltration Characterized by Upregulation of S100A8, S100A9, S100A12 and CXCR2 Is Associated With the Co-Occurrence of Crohn's Disease and Peripheral Artery Disease.. Frontiers in immunology, 2022. PMID 35795659. DOI 10.3389/fimmu.2022.896645.

Cautions

  • Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
  • Overall score capped because comparison suitability is weak for the selected search intent.
  • Comparison suitability score is below the Phase 1 recommended threshold.

Dataset Warnings

Normalized Fields

showing 500 of 1167 fields

Sample Group Preview

showing 51 of 251 preview rows Show Hide
Study totals: Case 250 | Control 1 | Unassigned 0 | Excluded 0 | Ambiguous 0 showing 51 of 251 preview rows
Group Role Accession Title Source / characteristics Reason
Crohn's disease Case GSM3043377 CSM5FZ1G Colon tissue Biopsy location: Sigmoid Colon; Disease status: Crohn's Disease; Gender: Female Case marker detected.
Crohn's disease Case GSM3043378 CSM5FZ1F Intestinal tissue Biopsy location: Ileum; Disease status: Crohn's Disease; Gender: Female Case marker detected.
Crohn's disease Case GSM3043379 CSM5FZ1I Rectum tissue Biopsy location: Rectum; Disease status: Crohn's Disease; Gender: Female Case marker detected.
Crohn's disease Case GSM3043380 CSM5FZ1H Colon tissue Biopsy location: Sigmoid Colon; Disease status: Crohn's Disease; Gender: Female Case marker detected.
Ulcerative colitis Case GSM3043381 CSM5FZ1J Intestinal tissue Biopsy location: Ileum; Disease status: Ulcerative Colitis; Gender: Female Case marker detected.
Ulcerative colitis Case GSM3043382 CSM5FZ1K Rectum tissue Biopsy location: Rectum; Disease status: Ulcerative Colitis; Gender: Female Case marker detected.
Ulcerative colitis Case GSM3043383 CSM5FZ1L Colon tissue Biopsy location: Sigmoid Colon; Disease status: Ulcerative Colitis; Gender: Female Case marker detected.
Ulcerative colitis Case GSM3043384 CSM5FZ1O Colon tissue Biopsy location: Sigmoid Colon; Disease status: Ulcerative Colitis; Gender: Female Case marker detected.
Ulcerative colitis Case GSM3043385 CSM5FZ1M Intestinal tissue Biopsy location: Ileum; Disease status: Ulcerative Colitis; Gender: Female Case marker detected.
Ulcerative colitis Case GSM3043386 CSM5FZ1N Rectum tissue Biopsy location: Rectum; Disease status: Ulcerative Colitis; Gender: Female Case marker detected.
Ulcerative colitis Case GSM3043387 CSM5FZ1Q Intestinal tissue Biopsy location: Ileum; Disease status: Ulcerative Colitis; Gender: Female Case marker detected.
Ulcerative colitis Case GSM3043388 CSM5FZ1R Rectum tissue Biopsy location: Rectum; Disease status: Ulcerative Colitis; Gender: Female Case marker detected.
Ulcerative colitis Case GSM3043389 CSM5FZ1S Colon tissue Biopsy location: Sigmoid Colon; Disease status: Ulcerative Colitis; Gender: Female Case marker detected.
Ulcerative colitis Case GSM3043390 CSM5FZ1W Colon tissue Biopsy location: Sigmoid Colon; Disease status: Ulcerative Colitis; Gender: Male Case marker detected.
Ulcerative colitis Case GSM3043391 CSM5FZ1T Intestinal tissue Biopsy location: Ileum; Disease status: Ulcerative Colitis; Gender: Male Case marker detected.
Ulcerative colitis Case GSM3043392 CSM5FZ1U Rectum tissue Biopsy location: Rectum; Disease status: Ulcerative Colitis; Gender: Male Case marker detected.
Ulcerative colitis Case GSM3043393 CSM5FZ1V Colon tissue Biopsy location: Sigmoid Colon; Disease status: Ulcerative Colitis; Gender: Male Case marker detected.
Crohn's disease Case GSM3043394 CSM5FZ22 Intestinal tissue Biopsy location: Ileum; Disease status: Crohn's Disease; Gender: Female Case marker detected.
Crohn's disease Case GSM3043395 CSM5FZ24 Rectum tissue Biopsy location: Rectum; Disease status: Crohn's Disease; Gender: Female Case marker detected.
Crohn's disease Case GSM3043396 CSM5FZ23 Colon tissue Biopsy location: Sigmoid Colon; Disease status: Crohn's Disease; Gender: Female Case marker detected.
Crohn's disease Case GSM3043397 CSM5FZ27 Intestinal tissue Biopsy location: Ileum; Disease status: Crohn's Disease; Gender: Female Case marker detected.
Crohn's disease Case GSM3043398 CSM5FZ28 Rectum tissue Biopsy location: Rectum; Disease status: Crohn's Disease; Gender: Female Case marker detected.
Crohn's disease Case GSM3043399 CSM5FZ29 Colon tissue Biopsy location: Sigmoid Colon; Disease status: Crohn's Disease; Gender: Female Case marker detected.
Ulcerative colitis Case GSM3043400 CSM5FZ2A Intestinal tissue Biopsy location: Ileum; Disease status: Ulcerative Colitis; Gender: Female Case marker detected.
Ulcerative colitis Case GSM3043401 CSM5FZ2B Rectum tissue Biopsy location: Rectum; Disease status: Ulcerative Colitis; Gender: Female Case marker detected.
Ulcerative colitis Case GSM3043402 CSM5FZ2C Colon tissue Biopsy location: Sigmoid Colon; Disease status: Ulcerative Colitis; Gender: Female Case marker detected.
Crohn's disease Case GSM3043403 CSM5FZ2D Intestinal tissue Biopsy location: Ileum; Disease status: Crohn's Disease; Gender: Female Case marker detected.
Crohn's disease Case GSM3043404 CSM5FZ2E Rectum tissue Biopsy location: Rectum; Disease status: Crohn's Disease; Gender: Female Case marker detected.
Crohn's disease Case GSM3043405 CSM5FZ2F Colon tissue Biopsy location: Sigmoid Colon; Disease status: Crohn's Disease; Gender: Female Case marker detected.
Ulcerative colitis Case GSM3043406 CSM5FZ2I Colon tissue Biopsy location: Sigmoid Colon; Disease status: Ulcerative Colitis; Gender: Female Case marker detected.
Ulcerative colitis Case GSM3043407 CSM5FZ2G Intestinal tissue Biopsy location: Ileum; Disease status: Ulcerative Colitis; Gender: Female Case marker detected.
Ulcerative colitis Case GSM3043408 CSM5FZ2H Rectum tissue Biopsy location: Rectum; Disease status: Ulcerative Colitis; Gender: Female Case marker detected.
Ulcerative colitis Case GSM3043409 CSM5FZ2N Intestinal tissue Biopsy location: Cecum; Disease status: Ulcerative Colitis; Gender: Female Case marker detected.
Ulcerative colitis Case GSM3043410 CSM5FZ2L Intestinal tissue Biopsy location: Ileum; Disease status: Ulcerative Colitis; Gender: Female Case marker detected.
Ulcerative colitis Case GSM3043411 CSM5FZ2M Rectum tissue Biopsy location: Rectum; Disease status: Ulcerative Colitis; Gender: Female Case marker detected.
Crohn's disease Case GSM3043412 CSM5FZ2O Intestinal tissue Biopsy location: Ileum; Disease status: Crohn's Disease; Gender: Female Case marker detected.
Crohn's disease Case GSM3043413 CSM5FZ2P Rectum tissue Biopsy location: Rectum; Disease status: Crohn's Disease; Gender: Female Case marker detected.
Crohn's disease Case GSM3043414 CSM5FZ2Q Colon tissue Biopsy location: Sigmoid Colon; Disease status: Crohn's Disease; Gender: Female Case marker detected.
Crohn's disease Case GSM3043415 CSM5FZ2R Intestinal tissue Biopsy location: Ileum; Disease status: Crohn's Disease; Gender: Male Case marker detected.
Crohn's disease Case GSM3043416 CSM5FZ2S Rectum tissue Biopsy location: Rectum; Disease status: Crohn's Disease; Gender: Male Case marker detected.
Crohn's disease Case GSM3043417 CSM5FZ2T Colon tissue Biopsy location: Sigmoid Colon; Disease status: Crohn's Disease; Gender: Male Case marker detected.
Crohn's disease Case GSM3043418 CSM5FZ36 Colon tissue Biopsy location: Descending (left-sided) colon; Disease status: Crohn's Disease; Gender: Female Case marker detected.
Crohn's disease Case GSM3043419 CSM5FZ34 Intestinal tissue Biopsy location: Ileum; Disease status: Crohn's Disease; Gender: Female Case marker detected.
Crohn's disease Case GSM3043420 CSM5FZ35 Rectum tissue Biopsy location: Rectum; Disease status: Crohn's Disease; Gender: Female Case marker detected.
Crohn's disease Case GSM3043421 CSM5FZ37 Intestinal tissue Biopsy location: Cecum; Disease status: Crohn's Disease; Gender: Female Case marker detected.
Inflammatory bowel disease Case GSM3043422 CSM5FZ38 Intestinal tissue Biopsy location: Ileum; Disease status: Non IBD; Gender: Male Case marker detected.
Inflammatory bowel disease Case GSM3043423 CSM5FZ39 Rectum tissue Biopsy location: Rectum; Disease status: Non IBD; Gender: Male Case marker detected.
Crohn's disease Case GSM3043424 CSM5FZ3A Intestinal tissue Biopsy location: Terminal ileum; Disease status: Crohn's Disease; Gender: Male Case marker detected.
Crohn's disease Case GSM3043425 CSM5FZ3B Rectum tissue Biopsy location: Ileum; Disease status: Crohn's Disease; Gender: Male Case marker detected.
Crohn's disease Case GSM3043426 CSM5FZ3C Rectum tissue Biopsy location: Rectum; Disease status: Crohn's Disease; Gender: Male Case marker detected.
200 additional case samples are hidden from this preview.
Non-inflamed tissue Control GSM3043543 HSM9JTC2 Tissue Biopsy location: Non-inflamed; Disease status: Ulcerative Colitis; Gender: Female 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.