← BioTransfer GEO Dataset Finder
GEO series

Transcriptomic profiles of biopsy-derived colon epithelial organoids from pediatric patients with ulcerative colitis

GSE276170 Homo sapiens (human) RNA-seq (gene expression) 48 samples Submitted 2025/09/19 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 48 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
48 samples: 6 conditions, mostly with about 8 replicates eachGroups 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.
Paper
Patient-derived colon epithelial organoids reveal lipid-related metabolic dysfunction in pediatric ulcerative colitisNature communications · 2025
Summary (written by the submitters)
Colon epithelial organoid lines were developed from pediatric patients with endoscopically active ulcerative colitis, inactive ulcerative colitis, and those without endoscopic or histologic evidence of colon inflammation (non-IBD controls). From each organoid line, RNA was processed from undifferentiated organoids (spheroids) and parallel organoids differentiated for 3 days (colonoids).
Read the full summary ↓
Paired-end sequencing of poly-A enriched RNA libraries was carried out on the Illumina NovaSeq PE150 platform and the reads were aligned to the human reference hg38 genome. To determine differentially expressed genes, transcripts with Log2FC ≥ ±1, FDR P ≤ 0.1 were considered statistically significant.
Published in
Patient-derived colon epithelial organoids reveal lipid-related metabolic dysfunction in pediatric ulcerative colitis
Ojo BA, Zhu Y, Heo L et al. · Nature communications 2025 · PMID 41372139 · doi:10.1038/s41467-025-65988-2
This dataset
Open GSE276170 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 GSE276170_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 PRJNA1155617 and SRA study SRP530021. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41372139) ↗
Study design
6 conditions, mostly with about 8 replicates each
non-IBD control, spheroids, C ×8 active UC, spheroids, aUC ×8 inactive UC, spheroids, iUC ×8 non-IBD control, colonoids, C ×8 active UC, colonoids, aUC ×8 inactive UC, colonoids, iUC ×8

Supports a between-group comparison across 48 samples.

How we read this: 6 replicated groups read from 48 sample titles; they account for 48 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.

Samples in this study

+ 8 more — browse all 48 samples with per-sample file links →

Datasets on a similar topic

Search all human RNA-seq datasets in GEO →

Share this dataset

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.