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Transcriptional effects of VIP on murine intestinal stem cells

GSE261001 Mus musculus (mouse) RNA-seq (gene expression) 37 samples Submitted 2024/09/27 Platform GPL19057
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: 31 distinct titles, 6 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
Vasoactive intestinal peptide promotes secretory differentiation and mitigates radiation-induced intestinal injuryStem cell research & therapy · 2024
Summary (written by the submitters)
In our study, we investigated the effect of Vasoactive intestinal peptide (VIP) on murine intestinal stem cell (ISC) activity and differentiation in homeostatic conditions and following irradiation-induced injury. We utilized a model of murine intestinal organoids and observed that VIP promotes epithelial differentiation towards a secretory phenotype predominantly via the p38 MAPK pathway.
Read the full summary ↓
Moreover, VIP prominently modulates epithelial proliferation as well as the number and proliferative activity of Lgr5-EGFP+ ISC under homeostatic conditions. Further analysis revealed that in vitro acute irradiation injury renders Lgr5-EGFP+ ISC even more susceptible to modulations by VIP, which results in the strong promotion of epithelial regeneration by VIP. Finally, these effects by VIP translate into an in vivo model of abdominal irradiation, where VIP was shown to prominently mitigate radiation-induced injury. Taken together, our findings indicate a prominent role of VIP in modulating ISC behavior in intestinal homeostasis and its potential to promote intestinal regeneration following acute irradiation injury.
Published in
Vasoactive intestinal peptide promotes secretory differentiation and mitigates radiation-induced intestinal injury
Agibalova T, Hempel A, Maurer HC et al. · Stem cell research & therapy 2024 · PMID 39380035 · doi:10.1186/s13287-024-03958-z
This dataset
Open GSE261001 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 GSE261001_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 PRJNA1084810 and SRA study SRP493671. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39380035) ↗
Study design
31 distinct titles, 6 of them repeated
m40061-control-BR1-T ×2 m40061-vip-BR1-T ×2 m40062-control-BR2-T ×2 m40062-vip-BR2-T ×2 m40065-vip-BR3-T ×2 m40066-vip-BR4-T ×2

How we read this: Read from 37 sample titles: 31 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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