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NOTCH-driven oscillations control cell fate decisions during intestinal homeostasis

GSE276270 Mus musculus (mouse) RNA-seq (gene expression) 36 samples Submitted 2025/09/01 Platform GPL19057
At a glance

RNA-seq (gene expression) · mouse · 36 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
36 samples: 12 conditions, mostly in triplicateGroups 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.
Summary (written by the submitters)
Intestinal homeostasis requires tight regulation of stem cell maintenance and commitment to absorptive and secretory cells, two key intestinal lineages1,2. While major signalling pathways critical for this control have been identified3, how they achieve such a tight balance in cell type composition remains unclear. Here, we uncover dynamic expression of Hes1, a direct NOTCH target3, in intestinal stem and progenitor cells, and investigate its role in vivo and in vitro.
Read the full summary ↓
A knock-in reporter4 reveals distinct, cell-specific period lengths in Hes1 oscillations that form a gradient along the crypt-villus axis. Whereas secretory precursors oscillate at low periods, absorptive precursors oscillate at higher periods before transitioning to a differentiated state. To test the function of different oscillation periods, we innovated a microfluidic system that modulates Hes1 oscillations in organoids. We find that varying the oscillation period modulates secretory cell differentiation: While 90-min oscillations promote Paneth cells, 130-min oscillations increase formation of other secretory subtypes. Moreover, low-period oscillations support stemness and a proliferative state. Our study provides the first clear evidence that information for tissue homeostasis in the intestine is encoded in the temporal dynamics of signalling components.
This dataset
Open GSE276270 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 GSE276270_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 PRJNA1156195 and SRA study SRP530299. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
12 conditions, mostly in triplicate
dapt-130min-72h-n ×3 dapt-170min-24h-n ×3 dapt-170min-48h-n ×3 dapt-170min-72h-n ×3 dapt-90min-24h-n ×3 dapt-90min-48h-n ×3 dapt-90min-72h-n ×3 dmso-24h-n ×3 +6 more

Supports a between-group comparison across 34 samples.

How we read this: 12 replicated groups read from 36 sample titles; they account for 34 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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