GEO series

Transcription factor ZNF263 primes human embryonic stem cells for pluripotency dissolution and early differentiation [ChIP-seq]

GSE242827 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 13 samples Submitted 2025/11/13 Platform GPL24676

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 13 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: 13 samples: 12 distinct titles, 1 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: Transcription factor ZNF263 primes human embryonic stem cells for pluripotency dissolution and lineage commitmentNature communications · 2025

Summary (written by the submitters)

Conventional human embryonic stem cells (hESCs) are capable of self-renewal and simultaneously poised for differentiation, and thus have been considered to resemble a primed pluripotent state. But the underlying regulatory mechanisms remain largely underexplored. Especially, little was known about the pivotal transcription factors (TFs) driving hESCs through the naïve-to-primed transition to prepare for differentiation.

Read the full summary ↓

Here, we conduct a large-scale in-silico screening and identify ZNF263 as a new key TF in primed hESCs, as evidenced by its extensive binding capacity at the active and poised genes. Genetic and functional assays reveal that ZNF263 directly initiates the incipient expression of early differentiation genes and concurrently dampens the core pluripotency circuitry in hESCs, greatly tilting the balance from pluripotency maintenance to lineage priming. Importantly, ZNF263 deficiency in hESCs further led to clear defects in pluripotency dissolution and lineage commitment, suggesting it’s indispensably required for the whole process. Together, our results demonstrate a pivotal role of ZNF263 in coordinating the establishment of primed pluripotency state in hESCs and facilitating the differentiation into primary germ layer lineages, which opens a new gate for understanding the central regulatory network governing human early development.

Published in

Transcription factor ZNF263 primes human embryonic stem cells for pluripotency dissolution and lineage commitment

Yin Q, Huang J, Sun H et al. · Nature communications 2025 · PMID 41193435 · doi:10.1038/s41467-025-64290-5

This dataset

Open GSE242827 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 GSE242827_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 PRJNA1014911 and SRA study SRP459532. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41193435) ↗

Study design

12 distinct titles, 1 of them repeated

H1, WT, ZNF263 ENDO ChIP, ×2

How we read this: Read from 13 sample titles: 12 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

GSM7771573 H1, WT, ZNF263 ENDO ChIP, rep1
GSM7771574 H1, WT, ZNF263 ENDO ChIP, rep2
GSM7771575 H1, WT, ZNF263 ENDO, input
GSM7771576 H1, 1-10 KO, ZNF263 FLAG ChIP
GSM7771577 H1, 1-10 KO, ZNF263 FLAG, input
GSM7771578 H1, WT, H3K4me3 ChIP
GSM7771579 H1, WT, H3K27ac ChIP
GSM7771580 H1, WT, H3K27me3 ChIP
GSM7771581 H1, WT, His, input
GSM7771582 H1, 1-10 KO, H3K4me3 ChIP
GSM7771583 H1, 1-10 KO, H3K27ac ChIP
GSM7771584 H1, 1-10 KO, H3K27me3 ChIP
GSM7771585 H1, 1-10 KO, His, input

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