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Whole transcriptome sequencing for upper tract urothelial carcinoma (UTUC) of BALB/c female mice treated with N-butyl-N-(4-hydroxybutyl) nitrosamine (BBN)

GSE274057 Mus musculus (mouse) RNA-seq (gene expression) 37 samples Submitted 2024/11/16 Platform GPL28457
At a glance

RNA-seq (gene expression) · mouse · 37 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
37 samples: 5 conditions, mostly with about 10 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
A novel mouse model of upper tract urothelial carcinoma highlights the impact of dietary intervention on gut microbiota and carcinogenesis prevention despite carcinogen exposureInternational journal of cancer · 2025
Summary (written by the submitters)
Only BALB/c female developed UTUC treated with BBN. To know the biological features of UTUC, we conducted the RNA-seq.
Published in
A novel mouse model of upper tract urothelial carcinoma highlights the impact of dietary intervention on gut microbiota and carcinogenesis prevention despite carcinogen exposure
Yamamoto A, Kawashima A, Uemura T et al. · International journal of cancer 2025 · PMID 39693209 · doi:10.1002/ijc.35295
This dataset
Open GSE274057 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 GSE274057_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 PRJNA1144834 and SRA study SRP524577. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39693209) ↗
Study design
5 conditions, mostly with about 10 replicates each
bladder treated with BBN ×10 cancer side of upper urinary tract treated wi… ×9 non-cancer side of upper urinary tract treate… ×7 normal upper urinary tract treated with tap w… ×6 normal bladder treated with tap wate ×3 cancer side of rt upper urinary tract treated… ×1 cancer side of lt upper urinary tract treated… ×1

Supports a between-group comparison across 35 samples.

How we read this: 5 replicated groups read from 37 sample titles; they account for 35 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

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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.