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NAC regulates metabolism and cell fate in intestinal stem cells

GSE230307 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2024/11/26 Platform GPL17021Platform GPL21626
At a glance

RNA-seq (gene expression) · mouse · 12 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
12 samples: 3 × RNAseq_SCd vs 3 × RiboSeq_L22_PD_SCd vs 3 × CRISPR_screen.T0 vs 3 × CRISPR_screen.T10Groups 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
NAC regulates metabolism and cell fate in intestinal stem cellsScience advances · 2025
Summary (written by the submitters)
mRNA translation is a highly dynamic process that has been shown to modulate cell adaptation to stress conditions. Upon ribosome impairment, ZAKα affects the metabolic profile of intestinal cells, however the mechanism by which this is promoted is still unclear. Here, we identified the nascent polypeptide-associated complex (NAC) as a central player in the metabolic regulation triggered by ribosome impairment.
Read the full summary ↓
Furthermore, we show that NAC is essential for the survival of the highly oxidative phosphorylation (OXPHOS) reliant intestinal stem cells (ISCs), being translationally regulated itself. NAC interacts with the ribosome and promotes the transport of the translation machinery and newly-formed peptides to the proximity of the mitochondria, allowing the import of proteins essential for processes such as OXPHOS. Upon translation stress, NAC is inhibited through an interaction with ZAKα, leading to the downregulation of OXPHOS. Overall, our findings unveil that NAC is a central player in translation-mediated metabolic regulation in intestinal cells.
Published in
NAC regulates metabolism and cell fate in intestinal stem cells
Ramalho S, Alkan F, Prekovic S et al. · Science advances 2025 · PMID 39772672 · doi:10.1126/sciadv.adn9750
This dataset
Open GSE230307 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 GSE230307_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 PRJNA958219 and SRA study SRP433785. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39772672) ↗
Study design
3 × RNAseq_SCd vs 3 × RiboSeq_L22_PD_SCd vs 3 × CRISPR_screen.T0 vs 3 × CRISPR_screen.T10

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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
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