GEO series

Transcriptomics of varying strength and timing of specific activation of the Integrated Stress Response

GSE273601 Homo sapiens (human) RNA-seq (gene expression) 60 samples Submitted 2024/08/28 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 60 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: Homo sapiens (human)
Samples: 60 samples: 20 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.
Paper: Specific activation of the integrated stress response uncovers regulation of central carbon metabolism and lipid droplet biogenesisNature communications · 2024

Summary (written by the submitters)

The integrated stress response (ISR) is a central signaling pathway induced by a variety of insults, but how its outputs contribute to downstream physiological effects across diverse cellular contexts remains unclear. Using a synthetic tool, we specifically and tunably activated the ISR and performed multi-omics profiling to define the core modules elicited by this response in the absence of co-activation of parallel pathways commonly induced by pleiotropic stressors.

Read the full summary ↓

We found that the ISR can elicit time- and dose-dependent gene expression changes that cluster into four modules with ATF4 driving only a small but fast and sensitive module that includes many amino acid metabolic enzymes. We showed that ATF4 was required to reroute carbon utilization towards amino acid synthesis derived both from glucose and reductive carboxylation of glutamine and away from the tricarboxylic acid cycle and fatty acid biogenesis revealing a new role for ATF4 in modulating cellular energetics. We also discovered an ATF4-independent reorganization of cellular lipids that promotes triglycerides synthesis and accumulation of lipid droplets that was essential for cell survival. Together, we demonstrate that a minimal ISR-inducing system is sufficient to trigger formation of two distinct cellular structures, stress granules and lipid droplets, and a previously unappreciated metabolic state.

Published in

Specific activation of the integrated stress response uncovers regulation of central carbon metabolism and lipid droplet biogenesis

Labbé K, LeBon L, King B et al. · Nature communications 2024 · PMID 39333061 · doi:10.1038/s41467-024-52538-5

This dataset

Open GSE273601 in finder → Find more human 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 GSE273601_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 PRJNA1142486 and SRA study SRP523369. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39333061) ↗

Study design

20 conditions, mostly in triplicate

DmrPERK, UT, 0h, ×3 DmrPERK, Dim .01 nM, 1h, ×3 DmrPERK, Dim .01 nM, 2h, ×3 DmrPERK, Dim .01 nM, 4h, ×3 DmrPERK, Dim .01 nM, 8h, ×3 DmrPERK, Dim .01 nM, 16h, ×3 DmrPERK, Dim .01 nM, 24h, ×3 DmrPERK, Dim .195 nM, 1h, ×3 +12 more

Supports a between-group comparison across 60 samples.

How we read this: 20 replicated groups read from 60 sample titles; they account for 60 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

GSM8433726 DmrPERK, UT, 0h, replicate 1 DmrPERK, UT, 0h,
GSM8433727 DmrPERK, UT, 0h, replicate 2 DmrPERK, UT, 0h,
GSM8433728 DmrPERK, UT, 0h, replicate 3 DmrPERK, UT, 0h,
GSM8433729 DmrPERK, Dim .01 nM, 1h, replicate 1 DmrPERK, Dim .01 nM, 1h,
GSM8433730 DmrPERK, Dim .01 nM, 1h, replicate 2 DmrPERK, Dim .01 nM, 1h,
GSM8433731 DmrPERK, Dim .01 nM, 1h, replicate 3 DmrPERK, Dim .01 nM, 1h,
GSM8433732 DmrPERK, Dim .01 nM, 2h, replicate 1 DmrPERK, Dim .01 nM, 2h,
GSM8433733 DmrPERK, Dim .01 nM, 2h, replicate 2 DmrPERK, Dim .01 nM, 2h,
GSM8433734 DmrPERK, Dim .01 nM, 2h, replicate 3 DmrPERK, Dim .01 nM, 2h,
GSM8433735 DmrPERK, Dim .01 nM, 4h, replicate 1 DmrPERK, Dim .01 nM, 4h,
GSM8433736 DmrPERK, Dim .01 nM, 4h, replicate 2 DmrPERK, Dim .01 nM, 4h,
GSM8433737 DmrPERK, Dim .01 nM, 4h, replicate 3 DmrPERK, Dim .01 nM, 4h,
GSM8433738 DmrPERK, Dim .01 nM, 8h, replicate 1 DmrPERK, Dim .01 nM, 8h,
GSM8433739 DmrPERK, Dim .01 nM, 8h, replicate 2 DmrPERK, Dim .01 nM, 8h,
GSM8433740 DmrPERK, Dim .01 nM, 8h, replicate 3 DmrPERK, Dim .01 nM, 8h,
GSM8433741 DmrPERK, Dim .01 nM, 16h, replicate 1 DmrPERK, Dim .01 nM, 16…
GSM8433742 DmrPERK, Dim .01 nM, 16h, replicate 2 DmrPERK, Dim .01 nM, 16…
GSM8433743 DmrPERK, Dim .01 nM, 16h, replicate 3 DmrPERK, Dim .01 nM, 16…
GSM8433744 DmrPERK, Dim .01 nM, 24h, replicate 1 DmrPERK, Dim .01 nM, 24…
GSM8433745 DmrPERK, Dim .01 nM, 24h, replicate 2 DmrPERK, Dim .01 nM, 24…
GSM8433746 DmrPERK, Dim .01 nM, 24h, replicate 3 DmrPERK, Dim .01 nM, 24…
GSM8433747 DmrPERK, Dim .195 nM, 1h, replicate 1 DmrPERK, Dim .195 nM, 1…
GSM8433748 DmrPERK, Dim .195 nM, 1h, replicate 2 DmrPERK, Dim .195 nM, 1…
GSM8433749 DmrPERK, Dim .195 nM, 1h, replicate 3 DmrPERK, Dim .195 nM, 1…
GSM8433750 DmrPERK, Dim .195 nM, 2h, replicate 1 DmrPERK, Dim .195 nM, 2…
GSM8433751 DmrPERK, Dim .195 nM, 2h, replicate 2 DmrPERK, Dim .195 nM, 2…
GSM8433752 DmrPERK, Dim .195 nM, 2h, replicate 3 DmrPERK, Dim .195 nM, 2…
GSM8433753 DmrPERK, Dim .195 nM, 4h, replicate 1 DmrPERK, Dim .195 nM, 4…
GSM8433754 DmrPERK, Dim .195 nM, 4h, replicate 2 DmrPERK, Dim .195 nM, 4…
GSM8433755 DmrPERK, Dim .195 nM, 4h, replicate 3 DmrPERK, Dim .195 nM, 4…
GSM8433756 DmrPERK, Dim .195 nM, 8h, replicate 1 DmrPERK, Dim .195 nM, 8…
GSM8433757 DmrPERK, Dim .195 nM, 8h, replicate 2 DmrPERK, Dim .195 nM, 8…
GSM8433758 DmrPERK, Dim .195 nM, 8h, replicate 3 DmrPERK, Dim .195 nM, 8…
GSM8433759 DmrPERK, Dim .195 nM, 16h, replicate 1 DmrPERK, Dim .195 nM, 1…
GSM8433760 DmrPERK, Dim .195 nM, 16h, replicate 2 DmrPERK, Dim .195 nM, 1…
GSM8433761 DmrPERK, Dim .195 nM, 16h, replicate 3 DmrPERK, Dim .195 nM, 1…
GSM8433762 DmrPERK, Dim .195 nM, 24h, replicate 1 DmrPERK, Dim .195 nM, 2…
GSM8433763 DmrPERK, Dim .195 nM, 24h, replicate 2 DmrPERK, Dim .195 nM, 2…
GSM8433764 DmrPERK, Dim .195 nM, 24h, replicate 3 DmrPERK, Dim .195 nM, 2…
GSM8433765 DmrPERK, UT 2, 0h, replicate 1 DmrPERK, UT 2, 0h,

+ 20 more — browse all 60 samples with per-sample file links →

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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.