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A set of Sox2-dependent OSN enhancers mediates the immediate response to neural induction and default neural differentiation of embryonic stem cells

GSE240327 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 40 samples Submitted 2024/04/04 Platform GPL30172Platform GPL24247
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 40 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
40 samples: 31 distinct titles, 9 of them repeatedGroups 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
Early neural specification of stem cells is mediated by a set of SOX2-dependent neural-associated enhancersStem cell reports · 2024
Summary (written by the submitters)
Sox2 is a transcription factor involved in the regulatory network maintaining the pluripotency of embryonic stem cells in culture as well as in early embryos. In addition, Sox2 plays a pivotal role in neural stem cell formation and neurogenesis. How Sox2 can serve both processes has remained elusive. Here we identified a set of Sox2-dependent neural associated enhancers (SONAE) activated immediately following neural induction and required in neural gene activation.
Read the full summary ↓
SONAE are a distinct subgroup (1898) of 8531 Oct4/Sox2/Nanog (OSN) bound enhancers, characterized by enhanced Sox2 binding and chromatin accessibility. SONAE activation is triggered by neural induction via Retinoic Acid treatment of wild type cells and is antagonized by mesodermal transcription factors repressing Sox2 following mesoderm induction. Neural differentiation is also set off by default in Smad4 ablated cells resistant to mesodermal induction. Our data provide mechanistic insight into the regulation of early neural versus mesodermal induction in ESCs and embryos.
Published in
Early neural specification of stem cells is mediated by a set of SOX2-dependent neural-associated enhancers
Tsaytler P, Blaess G, Scholze-Wittler M et al. · Stem cell reports 2024 · PMID 38579708 · doi:10.1016/j.stemcr.2024.03.003
This dataset
Open GSE240327 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 GSE240327_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 PRJNA1003385 and SRA study SRP453967. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38579708) ↗
Study design
31 distinct titles, 9 of them repeated
ATAC_DMSO_12h ×2 ATAC_DMSO_24h ×2 ATAC_dTAG13_12h ×2 ATAC_dTAG13_24h ×2 RNA_UT ×2 RNA_RA_3h_DMSO ×2 RNA_RA_6h_DMSO ×2 RNA_RA_12h_DMSO ×2 +1 more

How we read this: Read from 40 sample titles: 31 distinct titles with little repetition. 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

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