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TEAD2 mediates the ground-state pluripotency by chromatin looping

GSE226316 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 103 samples Submitted 2024/03/03 Platform GPL21273Platform GPL24247Platform GPL28330
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 103 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
103 samples: 42 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
TEAD2 initiates ground-state pluripotency by mediating chromatin loopingThe EMBO journal · 2024
Summary (written by the submitters)
Mouse embryonic stem cells (mESCs) cultured in 2i (MEK and GSK3 kinase inhibitor)/LIF and serum/LIF that we called 2i-ESCs and serum-ESCs represent ground and confused pluripotent states, respectively. However, the transcription factors that regulate ground pluripotency through chromatin-associated characteristics are not yet fully understood.
Read the full summary ↓
By mapping chromatin accessibility and transcription factor regulatory networks during the interconversion of 2i-ESCs and serum-ESCs, we have identified TEAD2 as highly enriched in 2i-specific peaks. While Tead2 knockout did not affect the pluripotency or differentiation ability of either 2i-ESCs or serum-ESCs, it did prevent the establishment of the 2i-specific state and the exit from the serum-specific state. TEAD2 binds to active regions in 2i-specific genes and activates their expression by regulating enhancer-promoter (EP) interactions during serum-to-2i transition. Remarkably, TEAD2-mediated EP interactions were independent of chromatin architecture proteins YY1 and CTCF, but instead appear to be facilitated by TEAD2 homodimer formation.
Published in
TEAD2 initiates ground-state pluripotency by mediating chromatin looping
Guo R, Dong X, Chen F et al. · The EMBO journal 2024 · PMID 38605224 · doi:10.1038/s44318-024-00086-5
This dataset
Open GSE226316 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 GSE226316_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 PRJNA939635 and SRA study SRP425027. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38605224) ↗
Study design
42 conditions, mostly in duplicate
2i_d3_RNAseq ×4 2i_ESCs_RNAseq ×4 serum_ESCs_RNAseq ×4 2i_d6_RNAseq ×3 2i_d12_RNAseq ×2 2i_d15_RNAseq ×2 2i_d3_ko_tead2_RNAseq ×2 2i_d6_ko_tead2_RNAseq ×2 +46 more

Supports a case/control comparison: 14 samples read as cases, 3 as controls.

How we read this: 42 replicated groups read from 103 sample titles; they account for 91 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

+ 63 more — browse all 103 samples with per-sample file links →

Datasets on a similar topic

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