← BioTransfer GEO Dataset Finder
GEO series

Reporter CRISPR screens decipher cis- and trans-regulatory principles at the Xist locus [RNA-seq]

GSE273071 Mus musculus (mouse) RNA-seq (gene expression) 59 samples Submitted 2025/05/21 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 59 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Mus musculus (mouse)
Samples
59 samples: 20 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
Summary (written by the submitters)
Developmental genes are controlled by several cis-acting regulatory elements (REs), which in turn respond to multiple trans-acting transcription factors (TFs). Understanding this regulatory complexity has remained a challenge. Here, we combine pooled CRISPR screens with different phenotypic readouts to dissect how a cis-regulatory landscape integrates information from a large number of TFs.
Read the full summary ↓
We apply our approach to the murine X-inactivation center, which harbors the Xist gene. We identify a large set of Xist-controlling TFs and map their TF-RE wiring at the Xist locus. We show that a transiently expressed group of XX-biased TFs, which includes the X-linked factor ZIC3, control Xist’s promoter-proximal REs. These factors promote initial Xist upregulation in a binary fashion, potentially ensuring female-specific Xist expression. A second set of developmental TFs, which include the epiblast master regulator of the epiblast OTX2, are upregulated slightly later and activate distal REs associated with the lncRNA genes Jpx, Ftx and Xert. We show that this second regulatory axis is required to ensure sufficiently high Xist RNA levels for efficient establishment of X-chromosome inactivation. Our unbiased, systematic approach provides a framework for the comprehensive dissection of regulatory interactions across genomic loci.
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 GSE273071 in finder → Find more mouse RNA-seq 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 GSE273071_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1139867 and SRA study SRP522073. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41053217) ↗
Study design
20 conditions, mostly in triplicate
RNA_XX_0h ×3 RNA_XX_10h ×3 RNA_XX_16h ×3 RNA_XX_24h ×3 RNA_XX_30h ×3 RNA_XX_36h ×3 RNA_XX_48h ×3 RNA_XX_56h ×3 +12 more

Supports a between-group comparison across 59 samples.

How we read this: 20 replicated groups read from 59 sample titles; they account for 59 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

+ 19 more — browse all 59 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq 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.