GEO series

Multiple subpopulations in medullary thymic epithelial cells are regulated by Aire with distinctive modes of gene regulations [CUT&Tag]

GSE206236 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 16 samples Submitted 2025/03/12 Platform GPL17021

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 16 samples

What it is: ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism: Mus musculus (mouse)
Samples: 16 samples: 8 conditions, mostly in duplicateGroups 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 combined single-cell multi-omics (scMulti-seq) technologies by which gene expression and open chromatin were simultaneously profiled from the same cell and deeper single-cell sequencing by RamDA-seq which enabled profiling of the minimum dropout. scMulti-seq effectively demonstrated the subpopulations among mTECs associated with diverse transcription factor activities which are affected by Aire and developmental stages, while RamDA-seq revealed the different modes of gene regulations by Aire in different subpopulations. Aire is not only essential for the development of a specific population in which Aire induces a set of genes in a stochastic manner but also promotes the development of multiple subpopulations in which Aire enhances the expressions of genes in a coordinated manner. The former group of Aire-induced genes was characterized by enhanced H3K27me3 chromatin modifications and Aire seems to unleash these silenced genes by deactivating polycomb repressive complex 2 (PRC2). We also found unique gene signatures for the neonatal stage such as high expression of chemokines and expression of cortical TEC (cTEC)-like genes in TECs, which were Aire-independent. Our approach has illuminated the multilayered transcriptional control in mTECs governing the multiple subpopulations organizing the thymic microenvironment.

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 GSE206236 in finder → Find more mouse ChIP / ATAC / CUT&Tag 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 GSE206236_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA849784 and SRA study SRP382011. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40244172) ↗

Study design

8 conditions, mostly in duplicate

WT, mTEChi, input, ×2 WT, mTEClo, input, ×2 AireKO, mTEChi, input, ×2 AireKO, mTEClo, input, ×2 WT, mTEChi, H3K27me3, ×2 WT, mTEClo, H3K27me3, ×2 AireKO, mTEChi, H3K27me3, ×2 AireKO, mTEClo, H3K27me3, ×2

Supports a between-group comparison across 16 samples.

How we read this: 8 replicated groups read from 16 sample titles; they account for 16 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

GSM6248543 WT, mTEChi, input, rep1 WT, mTEChi, input,
GSM6248544 WT, mTEChi, input, rep2 WT, mTEChi, input,
GSM6248545 WT, mTEClo, input, rep1 WT, mTEClo, input,
GSM6248546 WT, mTEClo, input, rep2 WT, mTEClo, input,
GSM6248547 AireKO, mTEChi, input, rep1 AireKO, mTEChi, input,
GSM6248548 AireKO, mTEChi, input, rep2 AireKO, mTEChi, input,
GSM6248549 AireKO, mTEClo, input, rep1 AireKO, mTEClo, input,
GSM6248550 AireKO, mTEClo, input, rep2 AireKO, mTEClo, input,
GSM6248551 WT, mTEChi, H3K27me3, rep1 WT, mTEChi, H3K27me3,
GSM6248552 WT, mTEChi, H3K27me3, rep2 WT, mTEChi, H3K27me3,
GSM6248553 WT, mTEClo, H3K27me3, rep1 WT, mTEClo, H3K27me3,
GSM6248554 WT, mTEClo, H3K27me3, rep2 WT, mTEClo, H3K27me3,
GSM6248555 AireKO, mTEChi, H3K27me3, rep1 AireKO, mTEChi, H3K27me…
GSM6248556 AireKO, mTEChi, H3K27me3, rep2 AireKO, mTEChi, H3K27me…
GSM6248557 AireKO, mTEClo, H3K27me3, rep1 AireKO, mTEClo, H3K27me…
GSM6248558 AireKO, mTEClo, H3K27me3, rep2 AireKO, mTEClo, H3K27me…

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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.