GEO series

Transfer RNA acetylation regulates in vivo mammalian stress signaling [tissues]

GSE284312 Mus musculus (mouse) RNA-seq (gene expression) 24 samples Submitted 2025/02/10 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 24 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: 24 samples: 6 conditions, mostly with about 4 replicates eachGroups 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: Transfer RNA acetylation regulates in vivo mammalian stress signalingScience advances · 2025

Summary (written by the submitters)

Transfer RNA (tRNA) modifications are crucial for protein synthesis, but their position-specific physiological roles remain poorly understood. Here, we investigate the impact of N4-acetylcytidine (ac4C), a highly conserved tRNA modification catalyzed by the essential acetyltransferase Nat10. By targeting Thumpd1, a nonessential adapter protein required for Nat10-catalyzed tRNA acetylation, we determine that loss of tRNA acetylation leads to reduced levels of tRNALeu, increased ribosome stalling, and activation of eIF2α phosphorylation.

Read the full summary ↓

Thumpd1 knockout mice exhibit growth defects and sterility. Concurrent knockout of Thumpd1 and the stress-sensing kinase Gcn2 causes penetrant postnatal lethality in mice, indicating a critical genetic interaction. Our findings demonstrate that a modification restricted to a single position within type II cytosolic tRNAs can regulate ribosome-mediated stress signaling in mammalian organisms, with implications for our understanding of translational control and therapeutic interventions.

Published in

Transfer RNA acetylation regulates in vivo mammalian stress signaling

Thalalla Gamage S, Khoogar R, Howpay Manage S et al. · Science advances 2025 · PMID 40106564 · doi:10.1126/sciadv.ads2923

This dataset

Open GSE284312 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 GSE284312_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 PRJNA1198508 and SRA study SRP551541. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40106564) ↗

Study design

6 conditions, mostly with about 4 replicates each

Liver Wildtype ×4 Liver Knockout ×4 Cerebellum Wildtype ×4 Cerebellum Knockout ×4 Testes Wildtype ×4 Testes Knockout ×4

Supports a case/control comparison: 12 samples read as cases, 12 as controls.

How we read this: 6 replicated groups read from 24 sample titles; they account for 24 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

GSM8682186 Liver Wildtype Replicate 1 Liver Wildtype
GSM8682187 Liver Wildtype Replicate 2 Liver Wildtype
GSM8682188 Liver Wildtype Replicate 3 Liver Wildtype
GSM8682189 Liver Wildtype Replicate 4 Liver Wildtype
GSM8682190 Liver Knockout Replicate 5 Liver Knockout
GSM8682191 Liver Knockout Replicate 6 Liver Knockout
GSM8682192 Liver Knockout Replicate 7 Liver Knockout
GSM8682193 Liver Knockout Replicate 8 Liver Knockout
GSM8682194 Cerebellum Wildtype Replicate 1 Cerebellum Wildtype
GSM8682195 Cerebellum Wildtype Replicate 2 Cerebellum Wildtype
GSM8682196 Cerebellum Wildtype Replicate 3 Cerebellum Wildtype
GSM8682197 Cerebellum Wildtype Replicate 4 Cerebellum Wildtype
GSM8682198 Cerebellum Knockout Replicate 5 Cerebellum Knockout
GSM8682199 Cerebellum Knockout Replicate 6 Cerebellum Knockout
GSM8682200 Cerebellum Knockout Replicate 7 Cerebellum Knockout
GSM8682201 Cerebellum Knockout Replicate 8 Cerebellum Knockout
GSM8682202 Testes Wildtype Replicate 1 Testes Wildtype
GSM8682203 Testes Wildtype Replicate 2 Testes Wildtype
GSM8682204 Testes Wildtype Replicate 3 Testes Wildtype
GSM8682205 Testes Wildtype Replicate 4 Testes Wildtype
GSM8682206 Testes Knockout Replicate 5 Testes Knockout
GSM8682207 Testes Knockout Replicate 6 Testes Knockout
GSM8682208 Testes Knockout Replicate 7 Testes Knockout
GSM8682209 Testes Knockout Replicate 8 Testes Knockout

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Search all mouse RNA-seq datasets in GEO →

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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.