GEO series

Stem-like T cells are associated with the pathogenesis of ulcerative colitis in humans [scRNAseq_Human]

GSE235663 Homo sapiens (human) Single-cell RNA-seq 18 samples Submitted 2024/04/24 Platform GPL24676

At a glance

Single-cell RNA-seq · human · 18 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)
Samples: 18 samples: 18 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.
Paper: Stem-like T cells are associated with the pathogenesis of ulcerative colitis in humansNature immunology · 2024

Summary (written by the submitters)

To understand the role of T cells in the pathogenesis of ulcerative colitis (UC), we analyzed colonic T cells isolated from UC patients and controls. We identified colonic CD4+ and CD8+ 32 T lymphocyte subsets with gene expression profiles resembling stem-like progenitors, previously reported in animal models of diabetes and other contexts.

Read the full summary ↓

Stem-like T cells were increased in inflamed areas compared to non-inflamed regions from the same patients. Furthermore, TCR sequence analysis indicated stem-like T cells were clonally related to pro-inflammatory T cells, suggesting their involvement in sustaining effectors that drive inflammation. Using an adoptive transfer colitis model, we demonstrated that CD4+ 38 T cells deficient in BCL-6, a transcription factor promoting T cell stemness, had decreased colon T cells, reduced TH17 cells, and diminished pathogenicity. Our results establish a strong association between stem-like T cell populations and UC pathogenesis, highlighting the potential of targeting this population to improve clinical outcomes.

Published in

Stem-like T cells are associated with the pathogenesis of ulcerative colitis in humans

Li Y, Ramírez-Suástegui C, Harris R et al. · Nature immunology 2024 · PMID 38898157 · doi:10.1038/s41590-024-01860-7

This dataset

Open GSE235663 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 GSE235663_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: 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 PRJNA986870 and SRA study SRP445515. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38898157) ↗

Study design

18 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 18 sample titles: 18 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

GSM7507204 006_10x_048_JiCh03_A_Gex
GSM7507205 007_10x_048_JiCh03_C_Gex
GSM7507206 008_10x_048_JiCh03_N_Gex
GSM7507207 009_10x_048_JiCh03_B_Gex
GSM7507208 010_10x_048_JiCh03_A_TCR
GSM7507209 011_10x_048_JiCh03_C_TCR
GSM7507210 012_10x_048_JiCh03_N_TCR
GSM7507211 013_10x_048_JiCh03_B_TCR
GSM7507212 014_10x_048_JiCh03_A_CITE
GSM7507213 015_10x_048_JiCh03_C_CITE
GSM7507214 016_10x_048_JiCh03_N_CITE
GSM7507215 017_10x_048_JiCh03_B_CITE
GSM7507216 10x_035_JiCh_CITE
GSM7507217 10x_035_JiCh_Gex
GSM7507218 10x_035_JiCh_TCR
GSM7507219 10x_042_JiCh02_CITE
GSM7507220 10x_042_JiCh02_Gex
GSM7507221 10x_042_JiCh02_TCR

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GSE245890 Analysis of rectal transcriptome in ulcerative colitis (UC) patients who received tofacitinib 51 samples shares ulcerative, colitis
GSE243625 Inflammatory transcriptomic signatures and cell type compositions in inflamed and non-inflamed colonic mucosa of ulcerative colitis 45 samples shares ulcerative, colitis
GSE288617 Paired transcriptomics reveals similarities between cytokine-stimulated organoids and ulcerative colitis epithelial responses 41 samples shares ulcerative, colitis
GSE266963 Tauroursodeoxycholic Acid (TUDCA) Reduces ER Stress and Lessens Disease Activity in Ulcerative Colitis 38 samples shares ulcerative, colitis

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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.