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Single-cell analysis reveals clonal expansions of pro-inflammatory tissue-resident memory Th17 cells in Crohn's disease

GSE247264 Homo sapiens (human) Single-cell RNA-seq 22 samples Submitted 2024/05/31 Platform GPL24676
At a glance

Single-cell RNA-seq · human · 22 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
22 samples: 7 × Lamina propria, Crohn's disease, biol vs 7 × Submucosa/muscularis propria, Crohn's disease, biol vs 4 × Lamina propria, Ulcerative colitis, biol vs 4 × Submucosa/muscularis propria, Ulcerative colitis, biolGroups 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
Characterization of Th17 tissue-resident memory cells in non-inflamed intestinal tissue of Crohn's disease patientsJournal of autoimmunity · 2024
Summary (written by the submitters)
To investigate the transcriptional profiles and functional characteristics of Trm cells in the small bowel of Crohn's disease (CD) and their interactions with immune cells, we performed single-cell RNA sequencing on CD3+ T cells and CD45+ immune cells.
Published in
Characterization of Th17 tissue-resident memory cells in non-inflamed intestinal tissue of Crohn's disease patients
Lee Y, Baek J, Park S et al. · Journal of autoimmunity 2024 · PMID 38554656 · doi:10.1016/j.jaut.2024.103206
This dataset
Open GSE247264 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 GSE247264_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 PRJNA1037014. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38554656) ↗
Study design
7 × Lamina propria, Crohn's disease, biol vs 7 × Submucosa/muscularis propria, Crohn's disease, biol vs 4 × Lamina propria, Ulcerative colitis, biol vs 4 × Submucosa/muscularis propria, Ulcerative colitis, biol

Supports a between-group comparison across 22 samples.

How we read this: 4 replicated groups read from 22 sample titles; they account for 22 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
Datasets on a similar topic

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