GEO series

Orchestration of pluripotent stem cell genome reactivation during mitotic exit [ChIP-Seq]

GSE241728 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 98 samples Submitted 2025/07/23 Platform GPL19057

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 98 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: 98 samples: 36 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: Orchestration of pluripotent stem cell genome reactivation during mitotic exitCell reports · 2025

Summary (written by the submitters)

The maintenance of cell identity faces many challenges during mitosis, as most DNA-binding proteins are evicted from DNA and transcription is virtually abolished. How cells maintain their identity through cell division and faithfully re-initiate gene expression during mitotic exit is unclear. Here, we developed a novel reporter system enabling cell cycle synchronization-free separation of pluripotent stem cells in temporal bins of < 30 minutes during mitotic exit.

Read the full summary ↓

This allowed us to quantify genome-wide reactivation of transcription, sequential changes in chromatin accessibility, and re-binding of the pluripotency transcription factors OCT4, SOX2, and NANOG (OSN). We found that transcriptional activity progressively ramped up after mitosis and that OSN rapidly reoccupied the genome during the anaphase-telophase transition. We also demonstrate transcription factor-specific, dynamic relocation patterns and a hierarchical reorganization of the OSN binding landscape governed by OCT4 and SOX2. Our study sheds light on the dynamic orchestration of transcriptional reactivation after mitosis.

Published in

Orchestration of pluripotent stem cell genome reactivation during mitotic exit

Placzek S, Vanzan L, Deluz C et al. · Cell reports 2025 · PMID 40153434 · doi:10.1016/j.celrep.2025.115486

This dataset

Open GSE241728 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 GSE241728_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 PRJNA1009417 and SRA study SRP457249. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40153434) ↗

Study design

36 conditions, mostly in duplicate

ChIP, Input, eG1-1, ×4 ChIP, Input, eG1-2, ×4 ChIP, Input, eG1-3, ×4 ChIP, Input, eG1-4, ×4 ChIP, Oct4, eG1-1, ×3 ChIP, Oct4, eG1-3, ×3 ChIP, Oct4, eG1-4, ×3 ChIP, Sox2, eG1-3, ×3 +42 more

Supports a between-group comparison across 84 samples.

How we read this: 36 replicated groups read from 98 sample titles; they account for 84 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

GSM7734433 ChIP, Input, NANOGOFF, rep1 ChIP, Input, NANOGOFF,
GSM7734434 ChIP, Input, NANOGOFF, rep2 ChIP, Input, NANOGOFF,
GSM7734435 ChIP, Input, NANOGON, rep1 ChIP, Input, NANOGON,
GSM7734436 ChIP, Input, NANOGON, rep2 ChIP, Input, NANOGON,
GSM7734437 ChIP, Input, OCT4OFF, rep1 ChIP, Input, OCT4OFF,
GSM7734438 ChIP, Input, OCT4OFF, rep2 ChIP, Input, OCT4OFF,
GSM7734439 ChIP, Input, OCT4ON, rep1 ChIP, Input, OCT4ON,
GSM7734440 ChIP, Input, OCT4ON, rep2 ChIP, Input, OCT4ON,
GSM7734441 ChIP, Nanog, NANOGOFF, rep1 ChIP, Nanog, NANOGOFF,
GSM7734442 ChIP, Nanog, NANOGOFF, rep2 ChIP, Nanog, NANOGOFF,
GSM7734443 ChIP, Nanog, NANOGON, rep1 ChIP, Nanog, NANOGON,
GSM7734444 ChIP, Nanog, NANOGON, rep2 ChIP, Nanog, NANOGON,
GSM7734445 ChIP, Nanog, OCT4OFF, rep1 ChIP, Nanog, OCT4OFF,
GSM7734446 ChIP, Nanog, OCT4OFF, rep2 ChIP, Nanog, OCT4OFF,
GSM7734447 ChIP, Nanog, OCT4ON, rep1 ChIP, Nanog, OCT4ON,
GSM7734448 ChIP, Nanog, OCT4ON, rep2 ChIP, Nanog, OCT4ON,
GSM7734449 ChIP, Nanog, SOX2OFF, rep1 ChIP, Nanog, SOX2OFF,
GSM7734450 ChIP, Nanog, SOX2OFF, rep2 ChIP, Nanog, SOX2OFF,
GSM7734451 ChIP, Nanog, SOX2ON, rep1 ChIP, Nanog, SOX2ON,
GSM7734452 ChIP, Nanog, SOX2ON, rep2 ChIP, Nanog, SOX2ON,
GSM7734453 ChIP, Oct4, NANOGOFF, rep1 ChIP, Oct4, NANOGOFF,
GSM7734454 ChIP, Oct4, NANOGOFF, rep2 ChIP, Oct4, NANOGOFF,
GSM7734455 ChIP, Oct4, NANOGON, rep1 ChIP, Oct4, NANOGON,
GSM7734456 ChIP, Oct4, NANOGON, rep2 ChIP, Oct4, NANOGON,
GSM7734457 ChIP, Oct4, OCT4OFF, rep1 ChIP, Oct4, OCT4OFF,
GSM7734458 ChIP, Oct4, OCT4OFF, rep2 ChIP, Oct4, OCT4OFF,
GSM7734459 ChIP, Oct4, OCT4ON, rep1 ChIP, Oct4, OCT4ON,
GSM7734460 ChIP, Oct4, OCT4ON, rep2 ChIP, Oct4, OCT4ON,
GSM7734461 ChIP, Sox2, NANOGOFF, rep1 ChIP, Sox2, NANOGOFF,
GSM7734462 ChIP, Sox2, NANOGOFF, rep2 ChIP, Sox2, NANOGOFF,
GSM7734463 ChIP, Sox2, NANOGON, rep1 ChIP, Sox2, NANOGON,
GSM7734464 ChIP, Sox2, NANOGON, rep2 ChIP, Sox2, NANOGON,
GSM7734465 ChIP, Sox2, OCT4OFF, rep1 ChIP, Sox2, OCT4OFF,
GSM7734466 ChIP, Sox2, OCT4OFF, rep2 ChIP, Sox2, OCT4OFF,
GSM7734467 ChIP, Sox2, OCT4ON, rep1 ChIP, Sox2, OCT4ON,
GSM7734468 ChIP, Sox2, OCT4ON, rep2 ChIP, Sox2, OCT4ON,
GSM7734469 ChIP, Sox2, SOX2OFF, rep1 ChIP, Sox2, SOX2OFF,
GSM7734470 ChIP, Sox2, SOX2OFF, rep2 ChIP, Sox2, SOX2OFF,
GSM7734471 ChIP, Sox2, SOX2ON, rep1 ChIP, Sox2, SOX2ON,
GSM7734472 ChIP, Sox2, SOX2ON, rep2 ChIP, Sox2, SOX2ON,

+ 58 more — browse all 98 samples with per-sample file links →

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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.