GEO series

Multimodal single cell analyses reveal mechanisms of perianal fistula in diverse Crohn’s disease [scRNA-seq]

GSE260842 Homo sapiens (human) Single-cell RNA-seq 34 samples Submitted 2024/05/16 Platform GPL24676

At a glance

Single-cell RNA-seq · human · 34 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: 34 samples: 34 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: Multimodal single-cell analyses reveal mechanisms of perianal fistula in diverse patients with Crohn's diseaseMed (New York, N.Y.) · 2024

Summary (written by the submitters)

Crohn’s disease (CD) is a chronic inflammatory condition that can affect any part of the gastrointestinal tract. African ancestry (AA) populations have been substantially under-represented in genome-wide association studies (GWAS) of CD and inflammatory bowel disease (IBD), reflecting in part the lower prevalence of CD in AA compared to European ancestry (EA) populations.

Read the full summary ↓

Importantly, CD complicated by perianal fistulae has been found to be more prevalent and severe in African-ancestry patients. Perianal fistulae arise from the distal rectal mucosa and can course to a cutaneous surface, resulting in highly morbid complications. Monoclonal antibodies against anti-TNF are the mainstay of treatment, but recurrence and secondary loss-of-response is common. In severe, uncontrolled cases, complete proctectomy is required. The intestine is unique among adult tissues in that under homeostasis, residential macrophages are continually replenished from recruited blood monocytes. In EA cohorts, we established that chronic monocyte cultures stimulated with NOD2 agonists result in aberrant myeloid-stromal differentiation stratified by risk allele carrier status. NOD2 risk alleles are not associated with perianal fistulae; African-American patients with CD do not carry them (except via recent European ancestry admixture). There is no direct association between known CD GWAS risk loci and the risk of developing perianal fistula. Here, we present direct ex-vivo, single cell multiomic analyses of colorectal tissues and perianal fistulous tracts in AA and EA cases to define mechanisms of perianal fistula development. We implicate myeloid-stromal crosstalk and define cell subtypes using single cell RNA (scRNASeq), ATAC sequencing, and chronic, unstimulated monocyte cultures. Transcription factor motifs and ATAC signals co-localized with fine-mapped GWAS loci provide insight to cell-specific and transcriptional network regulation.

Published in

Multimodal single-cell analyses reveal mechanisms of perianal fistula in diverse patients with Crohn's disease

Levantovsky RM, Tastad C, Zhang J et al. · Med (New York, N.Y.) 2024 · PMID 38663404 · doi:10.1016/j.medj.2024.03.021

This dataset

Open GSE260842 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 GSE260842_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 PRJNA1083604 and SRA study SRP493276. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38663404) ↗

Study design

34 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 34 sample titles: 34 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

GSM8125209 Perianal1_Sig_cytoRNA
GSM8125210 Perianal1_Transverse_cytoRNA
GSM8125211 Perianal2_Rect_cytoRNA
GSM8125212 Perianal2_Sig_cytoRNA
GSM8125213 Perianal3_Rect_cytoRNA
GSM8125214 Perianal3_Sig_cytoRNA
GSM8125215 Perianal2_Rect_cytoRNA_R
GSM8125216 Perianal2_Sig_cytoRNA_R
GSM8125217 Perianal3_Rect_cytoRNA_R
GSM8125218 Perianal3_Sig_cytoRNA_R
GSM8125219 Perianal4_Rect_cytoRNA
GSM8125220 Perianal4_TI_cytoRNA
GSM8125221 Perianal5_Rect_cytoRNA
GSM8125222 Perianal5_Sig_cytoRNA
GSM8125223 Perianal6_Rect_cytoRNA
GSM8125224 Perianal6_Sig_cytoRNA
GSM8125225 Perianal7_Rect_cytoRNA
GSM8125226 Perianal7_Sig_cytoRNA
GSM8125227 Perianal8_Rect_cytoRNA
GSM8125228 Perianal8_Sig_cytoRNA
GSM8125229 Perianal9_Rect_cytoRNA
GSM8125230 Perianal9_Sig_cytoRNA
GSM8125231 Perianal10_Rect_cytoRNA
GSM8125232 Perianal10_Sig_cytoRNA
GSM8125233 Perianal11_Rect_cytoRNA
GSM8125234 Perianal11_Fistula_cytoRNA
GSM8125235 Perianal12_Rect_cytoRNA
GSM8125236 Perianal12_Sig_cytoRNA
GSM8125237 Perianal13_Rect_cytoRNA
GSM8125238 Perianal13_Sig_cytoRNA
GSM8125239 Perianal14_Rect_cytoRNA
GSM8125240 Perianal14_Fistula_cytoRNA
GSM8125241 Perianal16_Fistula_cytoRNA
GSM8125242 Perianal16_Rect_cytoRNA

Datasets on a similar topic

GSE290220 TL1A-activated Tcells as upstream regulators of perianal fistulizing disease-associated changes in the rectum of Crohn's Disease patients [scRNA-seq] 29 samples shares scrna-seq, perianal, crohn
GSE269335 Single-cell multimodal profiling of monocytes reveals diverse phenotypes and alterations linked to cardiovascular disease risks 118 samples shares multimodal, diverse
GSE275145 Creeping fat-derived mechanosensitive fibroblasts drive intestinal fibrosis in Crohn’s disease strictures [Human scRNA-seq] 29 samples shares scrna-seq, crohn
GSE291014 TL1A-activated Tcells as upstream regulators of perianal fistulizing disease-associated changes in the rectum of Crohn's Disease patients [RNA-seq] 28 samples shares perianal, crohn
GSE305631 Spatially Resolved Insights Into Fistulating Crohn’s Disease Pathogenesis - bulk RNA-Seq 15 samples shares fistula, crohn
GSE253903 High-Dimensional Single-Cell Multimodal Landscape of Human Carotid Atherosclerosis [scRNA-seq] 12 samples shares multimodal, scrna-seq
GSE256490 Single-cell atlas of the human brain vasculature across development, adulthood and disease (scRNA-Seq) 71 samples shares scrna-seq
GSE317068 Multiscale analysis and functional validation of the cellular and genetic determinants of skeletal disease [Human scRNA-seq] 32 samples shares scrna-seq

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