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Gene suppression by PRC2 enhances the gene inductions by Aire and the development of mimetic cell populations

GSE249591 Mus musculus (mouse) RNA-seq (gene expression) 572 samples Submitted 2025/03/12 Platform GPL28457
At a glance

RNA-seq (gene expression) · mouse · 572 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
572 samples: 303 × mTEChi, neonate, EED-cKO, cell vs 97 × mTEChi, neonate, Aire/EED-dKO, cellGroups 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
Role of PRC2 in the stochastic expression of Aire target genes and development of mimetic cells in the thymusThe Journal of experimental medicine · 2025
Summary (written by the submitters)
Aire, a transcriptional regulator whose defect results in the development of autoimmunity, controls the transcriptome in the bulk of medullary thymic epithelial cells (mTECs) including the genes for self-antigens. Mechanisms for this process, however, remained incompletely understood, especially regarding the effects of Aire in each subpopulation in mTECs.
Read the full summary ↓
Here, we profiled mTECs from EED-cKO (EED conditional knockout mice using Foxn1-Cre, JACKSON LABORATORY #022727 and #018448) and Aire/EED-dKO (Aire EED double knockout mice, PMID: 19015306) by RamDA-seq to evaluate the association between the gene suppression by polycomb repressive complex 2 (PRC2) and the gene induction by Aire. We found that genes are suppressed by PRC2 in an Aire-independent manner in mTEC and the gene suppression by PRC2 paradoxically augments the gene inductions by Aire. Interestingly, PRC2 also suppresses the signature genes for mimetic cell populations and their development was diminished in the absence of EED.
Published in
Role of PRC2 in the stochastic expression of Aire target genes and development of mimetic cells in the thymus
Matsumoto M, Yoshida M, Oya T et al. · The Journal of experimental medicine 2025 · PMID 40244172 · doi:10.1084/jem.20240817
This dataset
Open GSE249591 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 GSE249591_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 PRJNA1049788 and SRA study SRP476817. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40244172) ↗
Study design
303 × mTEChi, neonate, EED-cKO, cell vs 97 × mTEChi, neonate, Aire/EED-dKO, cell

Supports a between-group comparison across 400 samples.

How we read this: 2 replicated groups read from the first 400 of 572 sample titles; they account for 400 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

+ 532 more — browse all 572 samples with per-sample file links →

Datasets on a similar topic

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