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Transcriptomics of specific activation of the Integrated Stress Response compared to Arsenite and Thapsigargin treatment

GSE273600 Homo sapiens (human) RNA-seq (gene expression) 120 samples Submitted 2024/08/28 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 120 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
120 samples: 40 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 GSE273600 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 GSE273600_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 PRJNA1142487 and SRA study SRP523372. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39333061) ↗
Study design
40 conditions, mostly in triplicate
Parental, UT, 0h, ×3 Parental, UT, 4h, ×3 Parental, UT, 8h, ×3 Parental, UT, 16h, ×3 Parental, UT, 24h, ×3 Parental, Dim .195 nM, 2h, ×3 Parental, Dim .195 nM, 4h, ×3 Parental, Dim .195 nM, 8h, ×3 +32 more

Supports a between-group comparison across 120 samples.

How we read this: 40 replicated groups read from 120 sample titles; they account for 120 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

+ 80 more — browse all 120 samples with per-sample file links →

Datasets on a similar topic

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