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Paired transcriptomics reveals similarities between cytokine-stimulated organoids and ulcerative colitis epithelial responses

GSE288617 Homo sapiens (human) RNA-seq (gene expression) 41 samples Submitted 2026/05/26 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 41 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
41 samples: 41 samples, each with a distinct title — no replicated groupsGroups 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.
Summary (written by the submitters)
The intestinal epithelium mediates critical crosstalk between microbiota and immune cells in inflammatory bowel disease. While patient-derived intestinal organoids offer potential for modeling ulcerative colitis, their ability to replicate in vivo inflammation and utility for precision medicine remain unclear.
Read the full summary ↓
By comparing transcriptomic profiles from microdissected colonic epithelium of ulcerative colitis patients with paired patient-derived organoids under various inflammatory conditions, we demonstrated that organoids established from uninflamed biopsies can effectively model epithelial inflammation. Combined IFNγ and TNF stimulation or a cocktail of pro- and anti-inflammatory signals induced inflammatory signatures matching in vivo ulcerative colitis patterns, including upregulation of interferon signaling, antigen presentation, and unfolded protein response pathways. Strong correlations between in vivo and in vitro expression of over 200 disease-relevant genes validate intestinal organoids as a suitable preclinical model. These findings substantiate intestinal epithelial organoids’ value for investigating ulcerative colitis pathogenesis and developing personalized medicine approaches.
This dataset
Open GSE288617 in finder → Find more human RNA-seq datasets →
Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE288617_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

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.

Raw reads on ENA ↗

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 PRJNA1218693. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
41 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 41 sample titles: 41 distinct titles with little repetition. 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.

Samples in this study

+ 1 more — browse all 41 samples with per-sample file links →

Datasets on a similar topic

Search all human RNA-seq datasets in GEO →

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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.