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BHLHE40 Orchestrates TL1A-Driven ILC3 Effector Programs and RORγt⁺ APC-Mediated Tolerance

GSE279193 Mus musculus (mouse) RNA-seq (gene expression) 24 samples Submitted 2026/07/06 Platform GPL34290Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 24 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
Mus musculus (mouse)
Samples
24 samples: 8 conditions, mostly in triplicateGroups 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)
A central feature of the intestinal immune system is the ability to protect against pathogens while maintaining antigen-specific tolerance to the gut bacteria that coat its surface. Here, we identified Bhlhe40 as a central regulator of both ILC3- and ROR t⁺ APC-dependent mucosal immunity. TL1A stimulation and inflammatory bowel disease both enhance Bhlhe40 expression in intestinal ILC3s.
Read the full summary ↓
Basal Bhlhe40 expression in ILC3s is essential for efficient transcription of cytokine effectors and maintenance of mucosal immunity, whereas TL1A-induced upregulation of Bhlhe40 further amplifies these effects. Bhlhe40 is also highly expressed in ROR t⁺ APCs, where it is required for optimal generation of antigen-specific Tregs. Together with the colonic microbiota, Bhlhe40 regulates expression of the co-stimulatory molecule Tnfsf4 (OX40L), which is necessary for the induction of Helicobacter hepaticus-specific Tregs. These findings reveal a previously unrecognized role for Bhlhe40 in orchestrating intestinal ILC3 responses and promoting Bhlhe40-dependent co-stimulatory signals in ROR t⁺ APCs that coordinate antigen-specific tolerance.
This dataset
Open GSE279193 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 GSE279193_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 PRJNA1171345 and SRA study SRP537730. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
8 conditions, mostly in triplicate
Bhlhe40 het_un ×3 Bhlhe40 ko_un ×3 Bhlhe40 het_TL1A ×3 Bhlhe40 ko_TL1A ×3 Bhlhe40 het_IL23 ×3 Bhlhe40 ko_IL23 ×3 un ×3 TL1A ×3

Supports a between-group comparison across 24 samples.

How we read this: 8 replicated groups read from 24 sample titles; they account for 24 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

Search all mouse 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.