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Global transcriptional profiles of mouse intestinal organoids treated with IFN-g or/and MEK inhibitor [RNA-Seq]

GSE282271 Mus musculus (mouse) RNA-seq (gene expression) 26 samples Submitted 2025/02/06 Platform GPL30172
At a glance

RNA-seq (gene expression) · mouse · 26 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
26 samples: 13 conditions, mostly in duplicateGroups 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
The balance between IFN-γ and ERK/MAPK signaling activities ensures lifelong maintenance of intestinal stem cellsCell reports · 2025
Summary (written by the submitters)
In this study, we found that it was possible to reflect age-associated changes of intestinal epithelium using the intestinal organoid system by modulating the balance between the IFN-g signaling and ERK/MAPK signaling pathways. To investigate the molecular mechanisms underlying the crosstalk between IFN-g and ERK/MAPK signaling pathways, we performed bulk RNA-seq on intestinal organoids treated with IFN-g and/or MEK inhibitor (iMEK).
Published in
The balance between IFN-γ and ERK/MAPK signaling activities ensures lifelong maintenance of intestinal stem cells
Nakajima-Koyama M, Kabata M, Lee J et al. · Cell reports 2025 · PMID 39952238 · doi:10.1016/j.celrep.2025.115286
This dataset
Open GSE282271 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 GSE282271_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 PRJNA1188023 and SRA study SRP546122. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39952238) ↗
Study design
13 conditions, mostly in duplicate
Intestinal_Organoids_0h ×2 Intestinal_Organoids_1h_Control ×2 Intestinal_Organoids_1h_IFNg ×2 Intestinal_Organoids_1h_iMEK ×2 Intestinal_Organoids_1h_IFNg_iMEK ×2 Intestinal_Organoids_6h_Control ×2 Intestinal_Organoids_6h_IFNg ×2 Intestinal_Organoids_6h_iMEK ×2 +5 more

Supports a between-group comparison across 26 samples.

How we read this: 13 replicated groups read from 26 sample titles; they account for 26 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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