← BioTransfer GEO Dataset Finder
GEO series

Effect of CRISPR activation of Zbtb7b, Vps72, Gba, or Mrpl9 in liver tumorigenesis in mice

GSE250070 Mus musculus (mouse) RNA-seq (gene expression) 30 samples Submitted 2025/01/01 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 30 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
30 samples: 6 conditions, mostly with about 5 replicates eachGroups 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 Activation Screening Reveals Chromosome 1q Genes VPS72, GBA1, and MRPL9 Drive Hepatocellular CarcinomaCellular and molecular gastroenterology and hepatology · 2025
Summary (written by the submitters)
Hepatocellular carcinomas (HCCs) undergo chromosomal amplifications with resultant increases in gene expression levels, yet the impact of these changes remains largely unknown. We sought to identify cancer driver genes at these genetic loci using CRISPR activation (CRISPRa) screening in mouse livers. We examined The Cancer Genome Atlas data for copy number-amplified and upregulated genes in HCCs.
Read the full summary ↓
We then conducted in vivo CRISPRa tumorigenesis screens targeting the top 51 genes using dCas9 knock-in mice. Genes Zbtb7b, Vps72, Gba, and Mrpl9 emerged as putative drivers of liver tumorigenesis. Furthermore, high levels of expression of VPS72, GBA, or MRPL9, but not ZBTB7B, correlated with worse survival of HCC patients from the The Cancer Genome Atlas. For validation of the role of these genes in driving tumorigenesis, mice were injected with single CRISPRa plasmids containing Vps72-, Gba-, or Mrpl9-targeting gRNAs. This led to decreased survival and extensive liver tumorigenesis compared to non-targeting controls. We performed RNA sequencing of these tumors to understand the transcriptomic changes caused by activation of these genes.
Published in
In Vivo CRISPR Activation Screening Reveals Chromosome 1q Genes VPS72, GBA1, and MRPL9 Drive Hepatocellular Carcinoma
Vázquez Salgado AM, Cai C, Lee M 2nd et al. · Cellular and molecular gastroenterology and hepatology 2025 · PMID 39761726 · doi:10.1016/j.jcmgh.2025.101460
This dataset
Open GSE250070 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 GSE250070_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 PRJNA1051973 and SRA study SRP477740. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39761726) ↗
Study design
6 conditions, mostly with about 5 replicates each
sg-NT_Bl ×6 sg-NT_Alb ×5 sg-Zbtb7b_Bl ×5 sg-Gba_Bl ×5 sg-Mrpl9_Bl ×5 sg-Vps72_Alb ×4

Supports a between-group comparison across 30 samples.

How we read this: 6 replicated groups read from 30 sample titles; they account for 30 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

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.