GEO series

A distinct cis-regulatory element is required for ILC3s to maintain intestinal tolerance through amplifying RORγt expression [scRNA-seq]

GSE274081 Mus musculus (mouse) Single-cell RNA-seq 2 samples Submitted 2026/08/06 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 2 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Mus musculus (mouse)
Samples: 2 samples: 2 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.

Summary (written by the submitters)

RORγt is the linage-specific transcription factor for both ILC3 and T-helper 17 (Th17) counterparts, who take an essential place in regulating intestinal homeostasis. While the biological significance of high RORγt expression and its distinct regulatory mechanisms in ILC3s remains investigation. Through comparing ATAC-seq results on ILC3 and Th17 cells, we identified an open chromatin region (OCR369) which specifically regulates ILC3 RORγt expression and development.

Read the full summary ↓

Mechanistically, OCR369 is bind by the RORγt activator RUNX3, and is also involved in the chromatin-loop formation between OCR369 and RORγt-promoter. OCR369 depletion also impaired the MHCII+ ILC3s, a group of antigen-presenting cells that regulate RORγt+ Treg cells. And disruption of Th/ Treg balance in the OCR369-deficient mice leads to the spontaneous type 2 inflammation in the small intestine, and impaired generation of oral tolerance. Thus, our study revealed a specific RORγt amplifying mechanism in ILC3 and its important role in maintaining intestinal immune environment and food tolerance.

This dataset

Open GSE274081 in finder → Find more mouse 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 GSE274081_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 PRJNA1144914 and SRA study SRP524529. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

2 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 2 sample titles: 2 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

GSM8443023 SI, 20w Naïve WT
GSM8443024 SI, 20w Naïve KO

Datasets on a similar topic

GSE325199 BHLHE40 Orchestrates TL1A-Driven ILC3 Effector Programs and RORγt⁺ APC-Mediated Tolerance. 40 samples shares ror, tolerance
GSE278157 A hierarchical Rorc(γt) cis-regulatory cascade orchestrates differentiation of RORγt⁺ innate immune cells [ATAC-seq] 40 samples shares ror, cis-regulatory
GSE269507 The interleukin 22–oncostatin M axis promotes intestinal inflammation and tumorigenesis [scRNA-seq] 12 samples shares intestinal, scrna-seq
GSE329635 Single-cell RNA sequencing of small intestinal organoid self-organization [scRNA-Seq] 10 samples shares intestinal, scrna-seq
GSE252027 Temporal co-regulation of microRNA arms among cell types after myocardial infarction [RNA-Seq] 96 samples shares ror
GSE318678 mRNA 3ʹ UTRs direct microRNA degradation to participate in imprinted gene networks and regulate growth dataset 6 48 samples shares ror
GSE296401 Interleukin-23 promotes a pro-inflammatory Th17 cell state by stabilizing RORγt and suppressing glucocorticoid receptor activity II 38 samples shares ror
GSE310456 Adipose tissue-derived microRNAs as epigenetic modulators of type 2 diabetes [DPDR_RNASEQ] 30 samples shares ror

Search all mouse RNA-seq datasets in GEO →

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