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In vivo CRISPR screen reveals interplay of epigenetic regulators underlies kinetics of hepatobiliary reprogramming [RNA-Seq]

GSE270509 Mus musculus (mouse) RNA-seq (gene expression) 27 samples Submitted 2025/01/01 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 27 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
27 samples: 6 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
In vivo CRISPR screening reveals epigenetic regulators of hepatobiliary plasticityGenes & development · 2025
Summary (written by the submitters)
Under chronic liver injury, a small fraction of hepatocytes undergoes reprogramming to biliary epithelial cells (BECs) through a multistep process of chromatin and transcriptional remodeling in which the hepatocyte phenotype is repressed and the biliary phenotype is activated. However, the epigenetic basis underlying this phenomenon is largely unknown. Here, we profiled cells after knockout of Nsd1 or Kdm2a at two reprogramming stages to assess the transcriptional differences imposed by epigenetic dysregulation.
Published in
In vivo CRISPR screening reveals epigenetic regulators of hepatobiliary plasticity
Sussman JH, Cure HW, Yuan S et al. · Genes & development 2025 · PMID 40169232 · doi:10.1101/gad.352420.124
This dataset
Open GSE270509 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 GSE270509_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 PRJNA1127022 and SRA study SRP515410. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40169232) ↗
Study design
6 conditions, mostly in triplicate
EV_Late_Reprogrammed ×7 EV_Early_Reprogrammed ×7 Kdm2aKO_Early_Reprogrammed ×4 Kdm2aKO_Late_Reprogrammed ×3 Nsd1KO_Early_Reprogrammed ×3 Nsd1KO_Late_Reprogrammed ×3

Supports a between-group comparison across 27 samples.

How we read this: 6 replicated groups read from 27 sample titles; they account for 27 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
Datasets on a similar topic

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