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Germline-somatic liaison dictates cancer subtype via de novo steroid biosynthesis

GSE293478 Homo sapiens (human) RNA-seq (gene expression) 29 samples Submitted 2025/06/03 Platform GPL16791
At a glance

RNA-seq (gene expression) · human · 29 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
Homo sapiens (human)
Topic
Prostate cancerThis series is part of our curated briefing on it.
Samples
29 samples: 27 distinct titles, 2 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
Germline-Somatic Liaison Dictates Cancer Subtypes via de novo Steroid BiosynthesisCancer discovery · 2025
Summary (written by the submitters)
This study investigates the cooperation between germline genetic variants and somatic mutations in prostate cancer. Specifically, we dissected the interplay between a germline variant at the 7p14.3 locus (rs1376350, G>A) and early recurrent prostate cancer-specific mutation in the Speckle-Type POZ protein (SPOP) gene across human prostate adenocarcinomas. The transcriptomes of multiple edited models pointed to Gli3 and the Hedgehog signaling pathway in a genotype-specific manner.
Published in
Germline-Somatic Liaison Dictates Cancer Subtypes via de novo Steroid Biosynthesis
Gasperini P, Alaimo A, Stringa B et al. · Cancer discovery 2025 · PMID 40512155 · doi:10.1158/2159-8290.CD-24-1904
This dataset
Open GSE293478 in finder → Find more human RNA-seq datasets → Prostate cancer landscape →
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 GSE293478_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 PRJNA1244773 and SRA study SRP575755. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40512155) ↗
Study design
27 distinct titles, 2 of them repeated
PC-3, clone 9, AA, ×2 PC-3, clone 1, AG, ×2

How we read this: Read from 29 sample titles: 27 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
More Prostate cancer datasets

Search all human RNA-seq datasets in GEO →

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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.