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Endonucleolytic RNA cleavage drives changes in gene expression during the innate immune response

GSE244125 Homo sapiens (human) RNA-seq (gene expression) 27 samples Submitted 2024/04/30 Platform GPL21290Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 27 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
27 samples: 8 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
Endonucleolytic RNA cleavage drives changes in gene expression during the innate immune responseCell reports · 2024
Summary (written by the submitters)
During viral infection, several dsRNA sensors are activated in the cell and trigger changes in gene expression. One of these sensors activates a generic endonuclease, RNase L, that cleaves many types of RNA in the cell. However, how the resultant widespread RNA decay affects gene expression is not fully understood. Here we found that gene expression changes caused by activating dsRNA sensing pathways are tuned by RNase L activation, pointing to an intricate antiviral response where multiple inputs are integrated to create an optimized output.
Read the full summary ↓
We show that RNA fragmentation induces the activation of the Ribotoxic Stress Response, potentially through ribosome collisions. The p38 and JNK pathways that are actuated as part of this response promote outcomes that likely inhibit the virus, such as programmed cell death. We also show that RNase L appears to limit the translation of genes that are regulated by another dsRNA-induced pathway, the Integrated Stress Response. Intriguingly, we found the activity of another generic endonuclease, RNase A, recapitulates many of the same molecular phenotypes as activated RNase L, demonstrating how widespread RNA cleavage events can directly evoke an antiviral program.
Published in
Endonucleolytic RNA cleavage drives changes in gene expression during the innate immune response
Karasik A, Lorenzi HA, DePass AV et al. · Cell reports 2024 · PMID 38823018 · doi:10.1016/j.celrep.2024.114287
This dataset
Open GSE244125 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 GSE244125_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 PRJNA1021271 and SRA study SRP463313. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38823018) ↗
Study design
8 conditions, mostly in triplicate
A549 human lung carcinoma, WT, 25A, ×5 A549 human lung carcinoma, WT, None, ×5 A549 human lung carcinoma, WT, polyIC, ×4 A549 human lung carcinoma, RNaseL_KO, 25A, ×3 A549 human lung carcinoma, RNaseL_KO, None, ×3 A549 human lung carcinoma, RNaseL_KO, polyIC, ×3 A549 human lung carcinoma, RNaseL_KO, Rnase A… ×2 A549 human lung carcinoma, RNaseL_KO, BSA ele… ×2

Supports a between-group comparison across 27 samples.

How we read this: 8 replicated groups read from 27 sample titles; they account for 27 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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