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Bulk RNAseq of Basal Cell Carcinoma (BCC) mouse models

GSE290008 Mus musculus (mouse) RNA-seq (gene expression) 21 samples Submitted 2025/03/18 Platform GPL30172
At a glance

RNA-seq (gene expression) · mouse · 21 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
21 samples: 6 conditions, mostly with about 4 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
Dissection of Gαs and Hedgehog Signaling Cross-talk Reveals Therapeutic Opportunities to Target Hedgehog-Dependent TumorsCancer research · 2026
Summary (written by the submitters)
RNA sequencing (RNAseq) of mouse tail keratinocytes from Basal Cell Carcinoma mouse models
Published in
Dissection of Gαs and Hedgehog Signaling Cross-talk Reveals Therapeutic Opportunities to Target Hedgehog-Dependent Tumors
Krantz S, Bell BA, Lund K et al. · Cancer research 2026 · PMID 41460725 · doi:10.1158/0008-5472.CAN-25-1109
This dataset
Open GSE290008 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 GSE290008_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 PRJNA1225727 and SRA study SRP565062. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41460725) ↗
Study design
6 conditions, mostly with about 4 replicates each
SmoM2_BCC ×4 Gnas-eKO_BCC ×4 PKI_BCC ×4 SmoM2_Con ×3 Gnas-eKO_Con ×3 PKI_Con ×3

Supports a between-group comparison across 21 samples.

How we read this: 6 replicated groups read from 21 sample titles; they account for 21 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 →

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