GEO series

Basis for Lineage-Determining Pioneer Factors Targeting Distinct Repressed Chromatin States

GSE299017 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 69 samples Submitted 2025/12/03 Platform GPL30882

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 69 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: 69 samples: 29 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: Basis for lineage-determining pioneer factors targeting distinct repressed chromatin statesScience advances · 2026

Summary (written by the submitters)

Pioneer transcription factors target compact, transcriptionally silent chromatin, thereby enabling gene activation in development, regeneration, and cell reprogramming. However, silent chromatin is heterogenous, varying in nucleosome mobility, nucleosome compaction, and repressive histone modifications, and how pioneer factors may overcome these different chromatin barriers is unknown.

Read the full summary ↓

We systematically compared the chromatin targeting of 13 embryonic transcription factors and found that the DNA binding domain (DBD) type predicts whether a pioneer factor targets low-turnover nucleosomes in compact chromatin, dynamic nucleosomes in compact chromatin, or function as non-pioneer factors targeting accessible chromatin. By contrast, non-DBD domains enable targeting of repressed chromatin marked by H3K9me3 or H3K27me3. Fusions of different non-DBD segments of heterochromatin-targeting pioneer factors onto SOX2 can expand binding of Sox2 target motifs, including within heterochromatin, and improve cellular reprogramming. Our study unveils how different forms of silent chromatin are coordinately targeted by lineage-specifying factors.

Published in

Basis for lineage-determining pioneer factors targeting distinct repressed chromatin states

Katznelson A, Zhang J, Donahue G et al. · Science advances 2026 · PMID 41512071 · doi:10.1126/sciadv.adz7409

This dataset

Open GSE299017 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 GSE299017_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 PRJNA1272117 and SRA study SRP589945. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41512071) ↗

Study design

29 conditions, mostly in duplicate

PAX3,V5,hBJ, ×3 PAX3,V5,hBJ,input ×3 SOX2ctESRRB,V5,hBJ, ×3 SOX2ctESRRB,V5,hBJ,input ×3 EBF1,V5,hBJ, ×2 EOMES,V5,hBJ, ×2 ESRRB,V5,hBJ, ×2 PAX7,V5,hBJ, ×2 +28 more

Supports a between-group comparison across 62 samples.

How we read this: 29 replicated groups read from 69 sample titles; they account for 62 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

GSM9030548 ASCL1,V5,hBJ,rep1
GSM9030549 ASCL1,V5,hBJ,input
GSM9030550 EBF1,V5,hBJ,rep1 EBF1,V5,hBJ,
GSM9030551 EBF1,V5,hBJ,rep2 EBF1,V5,hBJ,
GSM9030552 EBF1,V5,hBJ,input
GSM9030553 EOMES,V5,hBJ,rep1 EOMES,V5,hBJ,
GSM9030554 EOMES,V5,hBJ,rep2 EOMES,V5,hBJ,
GSM9030555 EOMES,V5,hBJ,input
GSM9030556 ESRRB,V5,hBJ,rep1 ESRRB,V5,hBJ,
GSM9030557 ESRRB,V5,hBJ,rep2 ESRRB,V5,hBJ,
GSM9030558 ESRRB,V5,hBJ,input
GSM9030559 PAX7,V5,hBJ,rep1 PAX7,V5,hBJ,
GSM9030560 PAX7,V5,hBJ,rep2 PAX7,V5,hBJ,
GSM9030561 PAX7,V5,hBJ,input1 PAX7,V5,hBJ,input
GSM9030562 PAX7,V5,hBJ,input2 PAX7,V5,hBJ,input
GSM9030563 PAX3,V5,hBJ,rep1 PAX3,V5,hBJ,
GSM9030564 PAX3,V5,hBJ,rep2 PAX3,V5,hBJ,
GSM9030565 PAX3,V5,hBJ,rep3 PAX3,V5,hBJ,
GSM9030566 PAX3,V5,hBJ,input1 PAX3,V5,hBJ,input
GSM9030567 PAX3,V5,hBJ,input2 PAX3,V5,hBJ,input
GSM9030568 PAX3,V5,hBJ,input3 PAX3,V5,hBJ,input
GSM9030569 RUNX1,V5,hBJ,rep1 RUNX1,V5,hBJ,
GSM9030570 RUNX1,V5,hBJ,rep2 RUNX1,V5,hBJ,
GSM9030571 RUNX1,V5,hBJ,input1 RUNX1,V5,hBJ,input
GSM9030572 RUNX1,V5,hBJ,input2 RUNX1,V5,hBJ,input
GSM9030573 PDX1,V5,hBJ,rep1 PDX1,V5,hBJ,
GSM9030574 PDX1,V5,hBJ,rep2 PDX1,V5,hBJ,
GSM9030575 PDX1,V5,hBJ,input1 PDX1,V5,hBJ,input
GSM9030576 PDX1,V5,hBJ,input2 PDX1,V5,hBJ,input
GSM9030577 TCF1,V5,hBJ,rep1 TCF1,V5,hBJ,
GSM9030578 TCF1,V5,hBJ,rep2 TCF1,V5,hBJ,
GSM9030579 TCF1,V5,hBJ,input
GSM9030580 SOX2,V5,hBJ,rep1 SOX2,V5,hBJ,
GSM9030581 SOX2,V5,hBJ,rep2 SOX2,V5,hBJ,
GSM9030582 SOX2,V5,hBJ,input1 SOX2,V5,hBJ,input
GSM9030583 SOX2,V5,hBJ,input2 SOX2,V5,hBJ,input
GSM9030584 ESRRBntSOX2,V5,hBJ,rep1 ESRRBntSOX2,V5,hBJ,
GSM9030585 ESRRBntSOX2,V5,hBJ,rep2 ESRRBntSOX2,V5,hBJ,
GSM9030586 ESRRBntSOX2,V5,hBJ,input1 ESRRBntSOX2,V5,hBJ,input
GSM9030587 ESRRBntSOX2,V5,hBJ,input2 ESRRBntSOX2,V5,hBJ,input

+ 29 more — browse all 69 samples with per-sample file links →

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Search all human ChIP / ATAC / CUT&Tag datasets in GEO →

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