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.
Single-cell RNA-seq · human · 13 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
- Organism
- Homo sapiens (human)
- Topic
- Colorectal cancerThis series is part of our curated briefing on it.
- Samples
- 13 samples: 7 × UC vs 6 × HCGroups 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
- OTUD3 prevents ulcerative colitis by inhibiting microbiota-mediated STING activationScience immunology · 2025
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 GSE296969_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.
Also filed as BioProject PRJNA1183559 and SRA study SRP555871. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 13 samples.
How we read this: 2 replicated groups read from 13 sample titles; they account for 13 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.
- GSM8980878 UC 3 UC
- GSM8980879 HC 1 HC
- GSM8980880 HC 2 HC
- GSM8980881 UC 6 UC
- GSM8980882 UC 4 UC
- GSM8980883 UC 5 UC
- GSM8980884 UC 2 UC
- GSM8980885 HC 4 HC
- GSM8980886 HC 6 HC
- GSM8980887 UC 1 UC
- GSM8980888 HC 5 HC
- GSM8980889 HC 3 HC
- GSM8980890 UC 7 UC
- GSE250000 Bulk RNA-sequencing of transduced colorectal cancer cell line HCT-116 and breast cancer cell line MCF-7 overexpressing full-lenght p53β or p53β-stop-lost. 4 samples same disease briefing · shares colorectal
- GSE12032 Inherent gene signature of stage II and III colorectal cancer leads in individual recurrence 198 samples same disease briefing · shares colorectal
- GSE109308 Single-cell transcriptomic survey of adenomatous polyposis patients with germline APC mutations 97 samples same disease briefing
- GSE110009 Single cell transcriptome landscape of primary and metastatic tumor in colon cancer 76 samples same disease briefing
- GSE243625 Inflammatory transcriptomic signatures and cell type compositions in inflamed and non-inflamed colonic mucosa of ulcerative colitis 45 samples shares ulcerative, inflamed, colitis
- GSE319878 Interrogating the mechanistic link between neighborhood deprivation and colorectal cancer risk through gene expression analysis of normal colorectal biopsies 171 samples shares colorectal, normal
- GSE292858 RNA-Seq analysis of tumor and matched normal samples from colorectal cancer patients. 73 samples shares colorectal, normal
- 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.