GEO series

FoxO transcription factors actuate the formative pluripotency specific gene expression programme [ChIP-Seq]

GSE253479 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 32 samples Submitted 2024/07/25 Platform GPL24247

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 32 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: 32 samples: 32 samples, each with a distinct title — no replicated groupsGroups 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: FoxO transcription factors actuate the formative pluripotency specific gene expression programmeNature communications · 2024

Summary (written by the submitters)

Naïve pluripotency is sustained by a self-reinforcing gene regulatory network (GRN) comprising core and naïve pluripotency-specific transcription factors (TFs). Upon exiting naïve pluripotency, ES cells transition through a formative post-implantation-like pluripotent state. However, the mechanisms underlying disengagement from the naïve GRN and initiation of the formative GRN remain unclear.

Read the full summary ↓

Here, we demonstrate that phosphorylated AKT acts as a gatekeeper that prevents nuclear localization of FoxO TFs in naïve ESCs. PTEN-mediated reduction of AKT activity allows nuclear entry by FoxO TFs, enforcing a cell fate transition by binding and activating formative pluripotency-specific enhancers. Indeed, FoxO TFs are necessary and sufficient for transition from the naïve to the formative pluripotent state. Our work uncovers a pivotal role for FoxO TFs and AKT signalling in mechanisms underlying the exit from naïve pluripotency, a critical early embryonic cell fate transition.

Published in

FoxO transcription factors actuate the formative pluripotency specific gene expression programme

Santini L, Kowald S, Cerron-Alvan LM et al. · Nature communications 2024 · PMID 39251582 · doi:10.1038/s41467-024-51794-9

This dataset

Open GSE253479 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 GSE253479_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 PRJNA1065872 and SRA study SRP484270. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39251582) ↗

Study design

32 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 32 sample titles: 32 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

GSM8021392 FoxO1, WT 2i, rep1, input
GSM8021393 FoxO1, Pten KO 2i, rep1, input
GSM8021394 FoxO1, WT 2i, rep2, input
GSM8021395 FoxO1, Pten KO 2i, rep2, input
GSM8021396 FoxO1, WT N24, rep1, input
GSM8021397 FoxO1, Pten KO N24, rep1, input
GSM8021398 FoxO1, WT N24, rep2, input
GSM8021399 FoxO1, Pten KO N24, rep2, input
GSM8021400 FoxO1, WT 2i, rep1, ChIP
GSM8021401 FoxO1, Pten KO 2i, rep1, ChIP
GSM8021402 FoxO1, WT 2i, rep2, ChIP
GSM8021403 FoxO1, Pten KO 2i, rep2, ChIP
GSM8021404 FoxO1, WT N24, rep1, ChIP
GSM8021405 FoxO1, Pten KO N24, rep1, ChIP
GSM8021406 FoxO1, WT N24, rep2, ChIP
GSM8021407 FoxO1, Pten KO N24, rep2,ChIP
GSM8021408 FoxO3, WT 2i, rep1, input
GSM8021409 FoxO3, Pten KO 2i, rep1, input
GSM8021410 FoxO3, WT N24, rep1, input
GSM8021411 FoxO3, Pten KO N24, rep1, input
GSM8021412 FoxO3, WT 2i, rep2, input
GSM8021413 FoxO3, Pten KO 2i, rep2, input
GSM8021414 FoxO3, WT N24, rep2, input
GSM8021415 FoxO3, Pten KO N24, rep2, input
GSM8021416 FoxO3, WT 2i, rep1, ChIP
GSM8021417 FoxO3, Pten KO 2i, rep1, ChIP
GSM8021418 FoxO3, WT N24, rep1, ChIP
GSM8021419 FoxO3, Pten KO N24, rep1, ChIP
GSM8021420 FoxO3, WT 2i, rep2, ChIP
GSM8021421 FoxO3, Pten KO 2i, rep2, ChIP
GSM8021422 FoxO3, WT N24, rep2, ChIP
GSM8021423 FoxO3, Pten KO N24, rep2,ChIP

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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.