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CTNNB1 mutations have diverse effects on signalling in Embryonic Stem Cells

GSE299075 Mus musculus (mouse) RNA-seq (gene expression) 25 samples Submitted 2025/11/06 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 25 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
25 samples: 20 distinct titles, 5 of them repeatedGroups 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
Mutational scanning reveals oncogenic CTNNB1 mutations have diverse effects on signalingNature genetics · 2026
Summary (written by the submitters)
Bulk 3' RNA-Seq was performed on Embronic Stem Cells (E14) to explore the diverse effect of CTNNB1 mutation alongside GSK3β inhibition via CHIR99021 serving as a positive control.
Published in
Mutational scanning reveals oncogenic CTNNB1 mutations have diverse effects on signaling
Krishna A, Meynert A, Dolt KS et al. · Nature genetics 2026 · PMID 41629672 · doi:10.1038/s41588-025-02496-5
This dataset
Open GSE299075 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 GSE299075_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 PRJNA1272532 and SRA study SRP590176. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41629672) ↗
Study design
20 distinct titles, 5 of them repeated
0uM_Chiron_E14 ×2 2.5uM_Chiron_E14 ×2 5uM_Chiron_E14 ×2 7_5uM_Chiron_E14 ×2 10uM_Chiron_E14 ×2

How we read this: Read from 25 sample titles: 20 distinct titles with little repetition. 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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