Multiple subpopulations in medullary thymic epithelial cells are regulated by Aire with distinctive modes of gene regulations
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 2219 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
- 2219 samples: 10 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
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE205411_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA844977 and SRA study SRP378239. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 350 samples.
How we read this: 10 replicated groups read from the first 400 of 2219 sample titles; they account for 350 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.
- GSM6211545 mTEClo, neonate, Ctrl, rep1 [EED_1]
- GSM6211546 mTEClo, neonate, Ctrl, rep2 [EED_2]
- GSM6211547 mTEClo, neonate, Ctrl, rep3 [EED_3]
- GSM6211548 mTEClo, neonate, EEDcKO, rep1 [EED_4]
- GSM6211549 mTEClo, neonate, EEDcKO, rep2 [EED_5]
- GSM6211550 mTEChi, neonate, Ctrl, rep1 [EED_6]
- GSM6211551 mTEChi, neonate, Ctrl, rep2 [EED_7]
- GSM6211552 mTEChi, neonate, Ctrl, rep3 [EED_8]
- GSM6211553 mTEChi, neonate, Ctrl, rep4 [EED_9]
- GSM6211554 mTEChi, neonate, Ctrl, rep5 [EED_10]
- GSM6211555 mTEChi, neonate, EEDcKO, rep1 [EED_11]
- GSM6211556 mTEChi, neonate, EEDcKO, rep2 [EED_12]
- GSM6211557 mTEChi, neonate, EEDcKO, rep3 [EED_13]
- GSM6211558 mTEChi, neonate, AireKO, rep1 [EED_14]
- GSM6211559 mTEChi, neonate, AireKO, rep2 [EED_15]
- GSM6211560 mTEChi, neonate, AireEEDdKO, rep1 [EED_16]
- GSM6211561 mTEChi, neonate, AireEEDdKO, rep2 [EED_17]
- GSM6211562 mTEChi, neonate, AireKO, rep3 [EED_18]
- GSM6211563 mTEChi, neonate, AireEEDdKO, rep3 [EED_19]
- GSM6211564 mTEClo, WT, rep1 [Aire_1]
- GSM6211565 mTEClo, WT, rep2 [Aire_2]
- GSM6211566 mTEClo, WT, rep3 [Aire_3]
- GSM6211567 mTEClo, WT, rep4 [Aire_4]
- GSM6211568 mTEClo, WT, rep5 [Aire_5]
- GSM6211569 mTEClo, WT, rep6 [Aire_6]
- GSM6211570 mTEClo, WT, rep7 [Aire_7]
- GSM6211571 mTEClo, WT, rep8 [Aire_8]
- GSM6211572 mTEClo, AireKO, rep1 [Aire_9]
- GSM6211573 mTEClo, AireKO, rep2 [Aire_10]
- GSM6211574 mTEClo, AireKO, rep3 [Aire_11]
- GSM6211575 mTEClo, AireKO, rep4 [Aire_12]
- GSM6211576 mTEChi, WT, rep1 [Aire_13]
- GSM6211577 mTEChi, WT, rep2 [Aire_14]
- GSM6211578 mTEChi, WT, rep3 [Aire_15]
- GSM6211579 mTEChi, WT, rep4 [Aire_16]
- GSM6211580 mTEChi, WT, rep5 [Aire_17]
- GSM6211581 mTEChi, WT, rep6 [Aire_18]
- GSM6211582 mTEChi, WT, rep7 [Aire_19]
- GSM6211583 mTEChi, AireKO, rep1 [Aire_20]
- GSM6211584 mTEChi, AireKO, rep2 [Aire_21]
+ 2179 more — browse all 2219 samples with per-sample file links →
- GSE205410 Multiple subpopulations in medullary thymic epithelial cells are regulated by Aire with distinctive modes of gene regulations [bulkRNA-seq] 47 samples shares subpopulations, distinctive, regulations, epithelial, medullary, multiple, thymic, modes
- GSE220665 The Transcriptional Cofactor SKI Regulates Medullary Thymic Epithelial Cell Differentiation and Peripheral T Cell Responses 42 samples shares epithelial, medullary, thymic
- GSE240020 Age-related epithelial defects limit thymic function and regeneration 51 samples shares epithelial, thymic
- GSE240016 Age-related epithelial defects limit thymic function and regeneration [single cell] 29 samples shares epithelial, thymic
- GSE240698 Thymic epithelial organoids mediate T cell development 11 samples shares epithelial, thymic
- GSE249753 Age-related epithelial defects limit thymic function and regeneration [single cell; Foxn1Lin] 3 samples shares epithelial, thymic
- GSE248586 A conserved epithelial wound-like transcriptional program driven by FOSL1 underlies malignant progression of pancreatic ductal adenocarcinoma 57 samples shares epithelial
- GSE276043 Glucocorticoids induce a maladaptive epithelial stress response to aggravate acute kidney injury 20 samples shares epithelial
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.