GEO series

COMPARATIVE SINGLE CELL PROFILING OF MUCOSA AND ORGANOIDS IMPLICATES ALTERED EPITHELIAL-MESENCHYMAL INTERACTIONS MEDIATED BY PTGER4 IN PERIANAL FISTULIZING CROHN’S DISEASE

GSE256497 Homo sapiens (human) Single-cell RNA-seq 44 samples Submitted 2024/11/22 Platform GPL24676

At a glance

Single-cell RNA-seq · human · 44 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: 44 samples: 31 × M vs 11 × O vs 2 × OUGroups 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: PTGER4 signaling regulates class IIa HDAC function and SPINK4 mRNA levels in rectal epithelial cellsCell communication and signaling : CCS · 2024

Summary (written by the submitters)

Background and aims: Perianal fistulizing Crohn’s disease (CD) is severe and often more difficult to treat than luminal CD. Current therapeutics focusing solely on the immune system neither target epithelial and mesenchymal compartments nor consider genetic/epigenetic mechanisms, potentially missing causative aspects of the disease. Thus, the mucosal cells and organoids from a cohort of perianal fistulizing CD patients and controls with diverse genetic backgrounds were experimentally examined.

Read the full summary ↓

Results: Overall, 140,503 mucosa and 77,044 organoid cells were sequenced. Inflamed perianal CD showed changes across the mucosal compartments (epithelium, immune, stromal), the most dramatic taking place in the epithelium. Epithelial changes occurring in the rectum of perianal CD patients associated with inflammation, gender, and ancestry, and were accompanied by a reduction in differentiated lineages. Organoids from the patient cohort retained both the gender- and ancestral-specific gene expression but did not overwhelmingly reflect their disease status. Organoids lacked bona fide differentiated lineages, but secretory pathways were promoted through PGE2-PTGER4 signaling and HDAC function. Conclusion: Epigenetic modifications are disrupted in the epithelium during inflammation and perianal fistulizing CD that affect the differentiation capacity of those cells, limiting their production/function and thus diminishing the ability of the patients’ mucosal tissue to heal. These epigenetic modifications appear to be modulated by crosstalk between the epithelial and mesenchymal cells, and thus might be leveraged therapeutically.

Published in

PTGER4 signaling regulates class IIa HDAC function and SPINK4 mRNA levels in rectal epithelial cells

Anbazhagan M, Sharma G, Murthy S et al. · Cell communication and signaling : CCS 2024 · PMID 39396982 · doi:10.1186/s12964-024-01879-1

This dataset

Open GSE256497 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 GSE256497_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 PRJNA1077718 and SRA study SRP490217. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39396982) ↗

Study design

31 × M vs 11 × O vs 2 × OU

Supports a between-group comparison across 44 samples.

How we read this: 3 replicated groups read from 44 sample titles; they account for 44 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

GSM8101846 M1 M
GSM8101847 M2 M
GSM8101848 M3 M
GSM8101849 M4 M
GSM8101850 M5 M
GSM8101851 M6 M
GSM8101852 M7 M
GSM8101853 M8 M
GSM8101854 M9 M
GSM8101855 M10 M
GSM8101856 M11 M
GSM8101857 M12 M
GSM8101858 M13 M
GSM8101859 M14 M
GSM8101860 M15 M
GSM8101861 M16 M
GSM8101862 M17 M
GSM8101863 M18 M
GSM8101864 M19 M
GSM8101865 M20 M
GSM8101866 M21 M
GSM8101867 M22 M
GSM8101868 M23 M
GSM8101869 M24 M
GSM8101870 M25 M
GSM8101871 M26 M
GSM8101872 M27 M
GSM8101873 M28 M
GSM8101874 M29 M
GSM8101875 M30 M
GSM8101876 M31 M
GSM8101877 OU1 OU
GSM8101878 OU2 OU
GSM8101879 O10 O
GSM8101880 O11 O
GSM8101881 O12 O
GSM8101882 O13 O
GSM8101883 O15 O
GSM8101884 O16 O
GSM8101885 O17 O

+ 4 more — browse all 44 samples with per-sample file links →

Datasets on a similar topic

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GSE307670 Epigenetic reprogramming of stromal cell states underpins pathologic tissue niches in Crohn’s disease 148 samples shares disease, crohn
GSE228360 Spatial and single cell transcriptomics reveals cellular crosstalk changes in ileal Crohn’s disease during inflammation 24 samples shares disease, crohn
GSE316782 Multimodal single-cell and spatial profiling reveals altered T cell-mediated immunity and B-cell follicular architecture in non-metastatic lymph nodes of patients with aggressive non-small cell lung cancer 18 samples shares mediated, altered
GSE280714 The role of RUNX2 and BHLHE40 in pathologically relevant CD4-positive tissue-resident T-cells in Crohn's disease. (scMultiome) 12 samples shares disease, crohn
GSE282122 A longitudinal single-cell atlas of anti-tumour necrosis factor treatment in inflammatory bowel disease 216 samples shares disease
GSE135251 TRANSCRIPTOMIC PROFILING ACROSS THE SPECTRUM OF NON-ALCOHOLIC FATTY LIVER DISEASE 216 samples shares disease

Search all human RNA-seq datasets in GEO →

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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.