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Impact of intestinal ERβ on the colon transcriptome during colitis-induced tumor development

GSE271135 Mus musculus (mouse) RNA-seq (gene expression) 38 samples Submitted 2025/07/21 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 38 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
38 samples: 8 conditions, mostly with about 5 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
Intestinal estrogen receptor beta modulates the murine colon tumor immune microenvironmentCancer letters · 2025
Summary (written by the submitters)
To understand how specifically intestinal ERβ impacts the transcriptome during colitis and tumor develpment, sequencing was perfromed on colon epithelium from AOM/DSS or vehicle treated mice, and tumors from treated mice.
Published in
Intestinal estrogen receptor beta modulates the murine colon tumor immune microenvironment
Birgersson M, Holm M, Gallardo-Dodd CJ et al. · Cancer letters 2025 · PMID 40120798 · doi:10.1016/j.canlet.2025.217661
This dataset
Open GSE271135 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 GSE271135_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 PRJNA1130036 and SRA study SRP517100. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40120798) ↗
Study design
8 conditions, mostly with about 5 replicates each
Female ERβKOVil, Vehicle, Scrape, ×5 Female ERβKOVil, AOM/DSS, 15 weeks, Scrape, ×5 Female WT, AOM/DSS, 15 weeks, Tumor, ×5 Male ERβKOVil, Vehicle, Scrape, ×5 Male ERβKOVil, AOM/DSS, 15 weeks, Scrape, ×5 Male WT, AOM/DSS, 15 weeks, Tumor, ×5 Female ERβKOVil, AOM/DSS, 15 weeks, Tumor, ×4 Male ERβKOVil, AOM/DSS, 15 weeks, Tumor, ×4

Supports a case/control comparison: 8 samples read as cases, 10 as controls.

How we read this: 8 replicated groups read from 38 sample titles; they account for 38 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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