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RNA structure directs RNA partitioning and is actively disrupted inside stress granules to enable cellular recovery

GSE288910 Homo sapiens (human) RNA-seq (gene expression) 126 samples Submitted 2025/12/31 Platform GPL34284Platform GPL18573Platform GPL20795
At a glance

RNA-seq (gene expression) · human · 126 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
126 samples: 52 conditions, mostly in duplicateGroups 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.
Summary (written by the submitters)
RNA structures play important roles in liquid-liquid phase separation. However, how it is regulated during stress response and stress granule formation is still under studied. Here, we performed in vivo RNA structure probing before and after sodium arsenite treatment, and in stress granules. While RNAs generally become more double-stranded upon stress, they maintain their single-strandedness inside stress granules.
Read the full summary ↓
We showed that RNA single-strandedness enables increased inclusion inside stress granules and that stress granule-enriched RNAs form fewer intra- and intermolecular RNA-RNA interactions. Additionally, several RNA binding proteins including SRSF1 are enriched in differential structure regions. eCLIP analysis revealed that SRSF1 binds to single-stranded regions along RNAs, and increased SRSF1 binding enabled better inclusion of RNAs in stress granules, whereas depletion of SRSF1 decreased stress granule formation under low amounts of stress. We also observed the active unwinding of RNAs inside stress granules by helicases, including DDX3X, and showed that inhibition of DDX3X results in slower dissolution of stress granules during recovery. Our study reveals the existence of multiple mechanisms to maintain RNA single-strandedness inside stress granules and to allow reversibility of stress granule formation, highlighting the importance of regulating RNA structure to enable cellular plasticity and response.
This dataset
Open GSE288910 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 GSE288910_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 PRJNA1219999 and SRA study SRP561964. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
52 conditions, mostly in duplicate
FracSHAPE, HeLa, Soluble Cytosol, Untreated, … ×3 FracSHAPE, HeLa, Soluble Cytosol, Untreated, … ×3 FracSHAPE, HeLa, RNA Granule, Untreated, DMSO, ×3 FracSHAPE, HeLa, RNA Granule, Untreated, NAIN… ×3 FracSHAPE, HeLa, Soluble Cytosol, NaAsO2, DMS… ×3 FracSHAPE, HeLa, Soluble Cytosol, NaAsO2, NAI… ×3 FracSHAPE, HeLa, RNA Granule, NaAsO2, DMSO, ×3 FracSHAPE, HeLa, RNA Granule, NaAsO2, NAIN3, ×3 +50 more

Supports a between-group comparison across 120 samples.

How we read this: 52 replicated groups read from 126 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

+ 86 more — browse all 126 samples with per-sample file links →

Datasets on a similar topic

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