← BioTransfer GEO Dataset Finder
GEO series

Identification and multimodal characterization of a specialized epithelial cell type associated with Crohn's Disease

GSE266546 Homo sapiens (human) RNA-seq (gene expression) 170 samples Submitted 2024/07/29 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 170 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
170 samples: 149 distinct titles, 14 of them repeatedGroups 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
Identification and multimodal characterization of a specialized epithelial cell type associated with Crohn's diseaseNature communications · 2024
Summary (written by the submitters)
Crohn’s disease (CD) is a complex chronic inflammatory disorder with both gastrointestinal and extra-intestinal manifestations associated immune dysregulation. Analyzing 202,359 cells from 170 specimens across 83 patients, we identified a distinct epithelial cell type in both terminal ileum and ascending colon (termed “LND”) with high expression of LCN2, NOS2, and DUOX2 and genes related to antimicrobial response and immunoregulation.
Read the full summary ↓
LND cells, confirmed by in-situ RNA and protein imaging, were rare in non-IBD controls but significantly expanded in active CD. These cells actively interacted with immune cells and specifically expressed IBD/CD susceptibility genes, as demonstrated by multimodal data, suggesting a possible role in CD immunopathogenesis. Furthermore, we discovered early and late LND subpopulations with different origins and developmental potential. A higher ratio of late to early LND cells correlated with better response to anti-TNF treatment. These findings suggest a potential pathogenic role for LND cells in both Crohn’s ileitis and colitis.
Published in
Identification and multimodal characterization of a specialized epithelial cell type associated with Crohn's disease
Li J, Simmons AJ, Hawkins CV et al. · Nature communications 2024 · PMID 39169060 · doi:10.1038/s41467-024-51580-7
This dataset
Open GSE266546 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 GSE266546_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 PRJNA1104768 and SRA study SRP505092. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39169060) ↗
Study design
149 distinct titles, 14 of them repeated
GCA211-Control-AC-Surgical ×5 GCA202-Control-AC-Surgical ×4 GCA055-Quiescent-AC-Endoscopy ×3 GCA211-Control-TI-Surgical ×3 GCA024-Control-AC-Endoscopy ×2 GCA119-Moderate-AC-Endoscopy ×2 GCA200-Severe-TI-Surgical ×2 GCA202-Control-TI-Surgical ×2 +6 more

How we read this: Read from 170 sample titles: 149 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

+ 130 more — browse all 170 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.