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Genome-binding/occupancy profiling of TNKS/PARP-inhibitor Regulated Naïve (TIRN) cells.

GSE291713 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 35 samples Submitted 2025/05/12 Platform GPL18573
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 35 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
35 samples: 17 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
Proteogenomic reprogramming to a functional human blastomere-like stem cell state via a PARP-DUX4 regulatory axisCell reports · 2025
Summary (written by the submitters)
Proteogenomic Reprogramming to a Functional Human Blastomere-like Stem Cell State via a PARP-DUX4 Regulatory Axis; Zimmerlin et al, 2024. PARP1 (ARTD1) and Tankyrases (TNKS1/TNKS2; PARP5a/5b) are poly-ADP-ribose polymerases (PARPs) with catalytic and non-catalytic functions that regulate both the genome and proteome during zygotic genome activation (ZGA) and pluripotent embryonic stages.
Read the full summary ↓
Here, we show that primed, conventional human pluripotent stem cells (hPSC) cultured continuously under non-specific TNKS1/TNKS2/PARP1-inhibited chemical naïve reversion conditions underwent proteogenomic reprogramming to a functional blastomere-like state. Tankyrase-PARP1 inhibitor-regulated naïve stem cells (TIRN-SC) concurrently expressed hundreds of gene targets of the ZGA-priming pioneer factor DUX4, as well as two- to eight-cell (2C-8C) (e.g., TPRXL, HOX clusters, EOMES, DUXA, GATA6), pre-lineage morula (e.g., GATA4, SOX17, FOXA2), and naïve epiblast (e.g., LEFTY2, DNMT3L, NANOG) lineage-specifying pioneer factors; all in a hybrid, single-cell manner. Mapping of the single-cell transcriptome of TIRN-SC to human embryo references identified populations expressing hybrid transcriptional programs that not only spanned 2C-4C (pre-ZGA) and morula-ICM stages, but that were also augmented following brief induction of DUX4 expression (iDUX4). Here, we performed ChIP-Seq profiling of PARP1, the core pluripotency factors NANOG, SOX2 and OCT4, phosphorylated-STAT3, BRD4 and modified histones H3K4me3, H3K27me3, H3K27ac. Co-binding analyses of core NANOG-SOX2-OCT4 (NSO) pluripotency factors with PARP1 (NSOP) identified genome-wide reprogramming of novel NSOP sites to DUX4-accessible distal and cis-regulatory enhancer regions in TIRN-SC. Gained NSOP enhancer regions possessed co-binding motifs for hundreds of the same 2C-8C-ICM-specific embryonic, and extraembryonic lineage-specifying pioneer factors (e.g., HOX, FOX, GATA, SOX, TBX families) that were concurrently co-expressed in TIRN-SC; suggesting that PARP1 and DUX4 chromatin co-binding cooperated with NSO core factors to regulate ZGA-associated lineage plasticity.
Published in
Proteogenomic reprogramming to a functional human blastomere-like stem cell state via a PARP-DUX4 regulatory axis
Zimmerlin L, Angarita A, Park TS et al. · Cell reports 2025 · PMID 40338744 · doi:10.1016/j.celrep.2025.115671
This dataset
Open GSE291713 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 GSE291713_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 PRJNA1235107 and SRA study SRP569800. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40338744) ↗
Study design
17 conditions, mostly in duplicate
RUES02, primed (E8), PARP1 ChIPseq, ×2 RUES02, TIRN (LIF-3i), PARP1 ChIPseq, ×2 RUES02, primed (E8), NANOG ChIPseq, ×2 RUES02, TIRN (LIF-3i), NANOG ChIPseq, ×2 RUES02, primed (E8), BRD4 ChIPseq, ×2 RUES02, TIRN (LIF-3i), BRD4 ChIPseq, ×2 RUES02, primed (E8), H3K27ac ChIPseq, ×2 RUES02, TIRN (LIF-3i), H3K27ac ChIPseq, ×2 +10 more

Supports a between-group comparison across 34 samples.

How we read this: 17 replicated groups read from 35 sample titles; they account for 34 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
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