Immune architecture of the colon in ICI-mediated colitis compared with ulcerative colitis
RNA-seq (gene expression) · human · 9 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Homo sapiens (human)
- Samples
- 9 samples: 3 × Ulcerative colitis vs 3 × Diarrhea only vs 3 × Immunotherapy colitisGroups are read from the sample names, not from the paper. Check the list below.
- Data you can get
- A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.
Processed table
The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE338317_RAW.tar (it can run to tens of gigabytes).
Raw sequencing reads
The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.
What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA1493239 and SRA study SRP717078. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 9 samples.
How we read this: 3 replicated groups read from 9 sample titles; they account for 9 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.
- GSM9871223 Ulcerative colitis 001 Ulcerative colitis
- GSM9871224 Diarrhea only 001 Diarrhea only
- GSM9871225 Ulcerative colitis 002 Ulcerative colitis
- GSM9871226 Diarrhea only 002 Diarrhea only
- GSM9871227 Diarrhea only 003 Diarrhea only
- GSM9871228 Ulcerative colitis 003 Ulcerative colitis
- GSM9871229 Immunotherapy colitis 001 Immunotherapy colitis
- GSM9871230 Immunotherapy colitis 002 Immunotherapy colitis
- GSM9871231 Immunotherapy colitis 003 Immunotherapy colitis
- GSE150115 Single-Cell Analyses of Colon and Blood Reveal Distinct Immune Cell Signatures of Ulcerative Colitis and Crohn’s Disease 5 samples shares ulcerative, colitis, colon
- GSE282580 Colon tissue gene expression associated with vedolizumab treatment effectiveness in ulcerative colitis. 60 samples shares ulcerative, colitis, colon
- GSE243625 Inflammatory transcriptomic signatures and cell type compositions in inflamed and non-inflamed colonic mucosa of ulcerative colitis 45 samples shares ulcerative, colitis, colon
- GSE224758 Gene expression profiling of colon biopsies from ulcerative colitis patients and healthy volunteers 22 samples shares ulcerative, colitis, colon
- GSE311760 IL-22 induces Paneth cell metaplasia in the colonic epithelium of ulcerative colitis, promoting wound healing via REG3A 18 samples shares ulcerative, colitis, colon
- GSE296969 Gene expression at single cell level of stromal cells from the distal colon of normal sites of colorectal cancer and inflamed sites of ulcerative colitis. 13 samples shares ulcerative, colitis, colon
- GSE334803 RNA sequencing of colonic tissues from ulcerative colitis patients and healthy controls 12 samples shares ulcerative, colitis, colon
- GSE190564 Divergent spatial microdomains drive inflammation and repair in Ulcerative and Immune Checkpoint Therapy Colitis - whole tissue scRNA-Seq 62 samples shares ulcerative, colitis
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.