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Transcriptomic characterization of Paneth-derived and Intestinal stem cell-derived murine intestinal tumors

GSE221819 Mus musculus (mouse) RNA-seq (gene expression) 15 samples Submitted 2024/03/27 Platform GPL28457
At a glance

RNA-seq (gene expression) · mouse · 15 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
15 samples: 15 samples, each with a distinct title — no replicated groupsGroups 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
Non-stem cell lineages as an alternative origin of intestinal tumorigenesis in the context of inflammationNature genetics · 2024
Summary (written by the submitters)
To investigate the effect of the cell-of-origin on the transcriptional phenotype of the tumor, we performed bulk RNAseq on macroscopically dissected intestinal tumors from mice carrying lineage-specific Apc/Kras mutations in Paneth or ISC cells. Where indicated, tumorigenisis was triggered in an inflammatory context by administration of Dextran Sodium Sulfate (DSS).
Published in
Non-stem cell lineages as an alternative origin of intestinal tumorigenesis in the context of inflammation
Verhagen MP, Joosten R, Schmitt M et al. · Nature genetics 2024 · PMID 38902475 · doi:10.1038/s41588-024-01801-y
This dataset
Open GSE221819 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 GSE221819_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 PRJNA916252 and SRA study SRP414937. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38902475) ↗
Study design
15 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 15 sample titles: 15 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
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.