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Transcriptional shut-off of MAP kinase signaling enables pluripotency maintenance during diapause

GSE249392 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 83 samples Submitted 2024/10/08 Platform GPL24247Platform GPL19057Platform GPL30172
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 83 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
83 samples: 17 conditions, mostly in triplicateGroups 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
The signaling cascade of induction and maintenance of ES cell diapauseResearch square · 2024
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
Published in
The signaling cascade of induction and maintenance of ES cell diapause
Tarakhovsky A, Zhang T, Marina R et al. · Research square 2024 · PMID 39281867 · doi:10.21203/rs.3.rs-4946357/v1
This dataset
Open GSE249392 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 GSE249392_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 PRJNA1048951 and SRA study SRP514003. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39281867) ↗
Study design
17 conditions, mostly in triplicate
Control for I-BETR ES cells ×4 I-BETR ES cells ×4 Control 60min DMSO ×3 WT control for 30min Torin1 treatment ×3 Torin1 treated 30min ×3 WT control for 60min Torin1 treatment ×3 Torin1 treated 60min ×3 WT control for 120min Torin1 treatment ×3 +39 more

Supports a case/control comparison: 12 samples read as cases, 40 as controls.

How we read this: 17 replicated groups read from 83 sample titles; they account for 53 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

+ 43 more — browse all 83 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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