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Reporter CRISPR screens decipher cis- and trans-regulatory principles at the Xist locus

GSE274507 synthetic construct; Mus musculus ChIP-seq / ATAC-seq (genome binding and open chromatin) 244 samples Submitted 2025/05/21 Platform GPL17769Platform GPL24247Platform GPL19057Platform GPL34475Platform GPL30172Platform GPL26526
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · synthetic construct; Mus musculus · 244 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
synthetic construct; Mus musculus
Samples
244 samples: 80 conditions, mostly in triplicateGroups 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
Reporter CRISPR screens decipher cis-regulatory and trans-regulatory principles at the Xist locusNature structural & molecular 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
Reporter CRISPR screens decipher cis-regulatory and trans-regulatory principles at the Xist locus
Schwämmle T, Noviello G, Kanata E et al. · Nature structural & molecular biology 2025 · PMID 41053217 · doi:10.1038/s41594-025-01686-3
This dataset
Open GSE274507 in finder → Find more 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 GSE274507_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 PRJNA1146897 and SRA study SRP522049. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41053217) ↗
Study design
80 conditions, mostly in triplicate
XX_D2_H3K27ac_sgNT ×3 XX_D2_H3K27ac_sgZic3 ×3 XX_D2_H3K27ac_sgNfrkb ×3 XX_D2_H3K27ac_sgOtx2 ×3 XX_D2_H3K27ac_sgFoxd3 ×3 XX_D2_H3K4me3_sgNT ×3 XX_D2_H3K4me3_sgZic3 ×3 XX_D2_H3K4me3_sgNfrkb ×3 +86 more

Supports a between-group comparison across 230 samples.

How we read this: 80 replicated groups read from 244 sample titles; they account for 230 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

+ 204 more — browse all 244 samples with per-sample file links →

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