GEO series

Poising and connectivity of emergent human developmental enhancers in the transition from naive to primed pluripotency - CUT&Tag

GSE309124 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 12 samples Submitted 2026/06/08 Platform GPL34295

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 12 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: Homo sapiens (human)
Samples: 12 samples: 6 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: Poising and connectivity of emergent human developmental enhancers in the transition from naive to primed pluripotencyCell reports · 2026

Summary (written by the submitters)

In primed human pluripotent stem cells (hPSCs) resembling post-implantation epiblast, numerous lineage-specific enhancers assume the poised chromatin state, co-marked by H3K4me1 and Polycomb-associated H3K27me3 histone modifications. In contrast, these poised enhancers (PEs) are scarce in naive hPSCs that model pre-implantation epiblast.

Read the full summary ↓

PEs form abundant chromosomal contacts with developmental genes, but when these contacts emerge, how their formation relates to enhancer poising and their functional significance remains incompletely understood. Here, we devise high-resolution, PE-targeted Capture Hi-C to generate a comprehensive atlas of PE chromosomal contacts in the time course of hPSC transition from the naive to primed state. We find that enhancer poising emerges early in the transition, while the contacts show diverse dynamics that is only partially coupled to poising. PROTAC-induced degradation of Polycomb Repressive Complex 2 (PRC2) early in the transition weakens PE connectivity, while inhibition of its H3K27 methyltransferase activity does not, suggesting a non-catalytic role of Polycomb in supporting PE contacts. Notably, PE contacts persist after developmental activation or ectopic CRISPRa targeting and can mediate long-range gene induction. Together, these findings reveal the temporal and mechanistic principles of PE connectivity, highlighting a potential role of PE contacts in establishing gene expression patterns in human development.

Published in

Poising and connectivity of emergent human developmental enhancers in the transition from naive to primed pluripotency

Nocente MC, Della Rosa M, Malcolm AA et al. · Cell reports 2026 · PMID 42250221 · doi:10.1016/j.celrep.2026.117402

This dataset

Open GSE309124 in finder → Find more human 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 GSE309124_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 PRJNA1334003 and SRA study SRP626450. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42250221) ↗

Study design

6 conditions, mostly in duplicate

DMSO_H2AK119ub ×2 DMSO_H3K27me3 ×2 PROTAC_H2AK119ub ×2 PROTAC_H3K27me3 ×2 UNC_H2AK119ub ×2 UNC_H3K27me3 ×2

Supports a between-group comparison across 12 samples.

How we read this: 6 replicated groups read from 12 sample titles; they account for 12 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

GSM9261495 DMSO_H2AK119ub_Rep1 DMSO_H2AK119ub
GSM9261496 DMSO_H2AK119ub_Rep2 DMSO_H2AK119ub
GSM9261497 DMSO_H3K27me3_Rep1 DMSO_H3K27me3
GSM9261498 DMSO_H3K27me3_Rep2 DMSO_H3K27me3
GSM9261499 PROTAC_H2AK119ub_Rep1 PROTAC_H2AK119ub
GSM9261500 PROTAC_H2AK119ub_Rep2 PROTAC_H2AK119ub
GSM9261501 PROTAC_H3K27me3_Rep2 PROTAC_H3K27me3
GSM9261502 UNC_H2AK119ub_Rep1 UNC_H2AK119ub
GSM9261503 UNC_H2AK119ub_Rep2 UNC_H2AK119ub
GSM9261504 UNC_H3K27me3_Rep1 UNC_H3K27me3
GSM9261505 UNC_H3K27me3_Rep2 UNC_H3K27me3
GSM9602200 PROTAC_H3K27me3_Rep1 PROTAC_H3K27me3

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