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Full-length direct RNA sequencing uncovers stress-granule dependent RNA decay upon cellular stress

GSE204785 Homo sapiens (human) RNA-seq (gene expression) 39 samples Submitted 2024/11/14 Platform GPL26624Platform GPL26167Platform GPL24106
At a glance

RNA-seq (gene expression) · human · 39 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
39 samples: 12 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.
Paper
Full-length direct RNA sequencing uncovers stress-granule dependent RNA decay upon cellular stressbioRxiv : the preprint server for biology · 2024
Summary (written by the submitters)
To investigate the role of oxidative stress on RNA dynamics, we treatd HeLa cell lines with 500 µM of arsenite. We then explored the role of XRN1, CHX and ISRIB on mRNA shrotening using the data obtained from dRNA seq
Published in
Full-length direct RNA sequencing uncovers stress-granule dependent RNA decay upon cellular stress
Dar SA, Malla S, Martinek V et al. · bioRxiv : the preprint server for biology 2024 · PMID 37693505 · doi:10.1101/2023.08.31.555629
This dataset
Open GSE204785 in finder → Find more 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 GSE204785_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 PRJNA842344 and SRA study SRP377022. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 37693505) ↗
Study design
12 conditions, mostly in duplicate
HeLa cells, Arsenite, 60 min, ×3 HeLa cells, ×3 HeLa cells, Arsenite, Cycloheximide, 60 min, ×2 HeLa cells, Arsenite, Dimethyl sulfoxide, 60 … ×2 HeLa cells, Arsenite, ISRIB, 60 min, ×2 HeLa cells, Cycloheximide, ×2 HeLa cells, Dimethyl sulfoxide, ×2 HeLa cells, ISRIB, ×2 +17 more

Supports a between-group comparison across 26 samples.

How we read this: 12 replicated groups read from 39 sample titles; they account for 26 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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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.