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Loss of PI5P4Kα slows the progression of a Pten mutant basal cell model of prostate cancer

GSE277842 Mus musculus (mouse) Single-cell RNA-seq 18 samples Submitted 2024/09/24 Platform GPL19057
At a glance

Single-cell RNA-seq · mouse · 18 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Mus musculus (mouse)
Samples
18 samples: 8 conditions, mostly in duplicateGroups 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
Loss of PI5P4Kα Slows the Progression of a Pten Mutant Basal Cell Model of Prostate CancerMolecular cancer research : MCR · 2025
Summary (written by the submitters)
We use in vivo mouse models to characterize the outcome of deleting PI5P4Kα in prostate basal cells. Single cell RNA-Seq analysis reveals the molecular consequence of altering PI5P4Kα and links impaired lipid metabolism with delayed mPIN development.
Published in
Loss of PI5P4Kα Slows the Progression of a Pten Mutant Basal Cell Model of Prostate Cancer
Triscott J, Lehner M, Benjak A et al. · Molecular cancer research : MCR 2025 · PMID 39382632 · doi:10.1158/1541-7786.MCR-24-0290
This dataset
Open GSE277842 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 GSE277842_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1164311 and SRA study SRP534284. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39382632) ↗
Study design
8 conditions, mostly in duplicate
basal CK5eYFP, 2m, mouse 1, plate ×3 basal CK5eYFP, 2m, mouse 2, plate ×3 basal CK5eYFP, 2w, mouse 1, plate ×2 luminal PBeYFP, 2w, mouse 2, plate ×2 luminal PBeYFP, 2w, mouse 1, plate ×2 basal CK5eYFP, 2w, mouse 2, plate ×2 basal CK5PIP, 2m, mouse 1, plate ×2 basal CK5PIP, 2m, mouse 2, plate ×2

Supports a between-group comparison across 18 samples.

How we read this: 8 replicated groups read from 18 sample titles; they account for 18 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
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