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The role of HNRNPU and the nuclear matrix in human pluripotent stem cells

GSE242351 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 78 samples Submitted 2024/11/05 Platform GPL24676
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 78 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
78 samples: 31 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
The nuclear matrix stabilizes primed-specific genes in human pluripotent stem cellsNature cell biology · 2025
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
Published in
The nuclear matrix stabilizes primed-specific genes in human pluripotent stem cells
Ma G, Fu X, Zhou L et al. · Nature cell biology 2025 · PMID 39789220 · doi:10.1038/s41556-024-01595-5
This dataset
Open GSE242351 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 GSE242351_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 PRJNA1013371 and SRA study SRP458883. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39789220) ↗
Study design
31 conditions, mostly in duplicate
hPSC RNA-seq shLUC Repeat ×8 hPSC RNA-seq shMATR3 Repeat ×4 hPSC RNA-seq shHNRNPU#1 Repeat ×3 hPSC RNA-seq shHNRNPU#2 Repeat ×3 ATAC-seq shHNRNPU #1 repeat ×2 ATAC-seq shHNRNPU #2 repeat ×2 ATAC-seq shLUC #1 repeat ×2 H3K4me1 (CUT&TAG) shHNRNPU#1 repeat ×2 +29 more

Supports a between-group comparison across 72 samples.

How we read this: 31 replicated groups read from 78 sample titles; they account for 72 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

+ 38 more — browse all 78 samples with per-sample file links →

Datasets on a similar topic

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

Share this dataset

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.