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Spatially resolved multi-bait mapping of stress granule and processing body transcriptome

GSE271045 Homo sapiens (human) RNA-seq (gene expression) 24 samples Submitted 2024/09/29 Platform GPL20795
At a glance

RNA-seq (gene expression) · human · 24 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
24 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.
Summary (written by the submitters)
Stress granules (SGs) are dynamic, membrane-less organelles containing complex RNA-protein networks. The RNA components of SGs have been profiled through various approaches, characterized as long, translation-repressed, and highly epigenetically modified. However, it remains unclear whether these RNAs are uniformly distributed within SGs.
Read the full summary ↓
In this study, we used multiple SG core proteins to genetically target the photocatalyst protein miniSOG, which allows for comprehensive CAP-seq profiling of RNA components within SGs. We discovered that RNAs associated with different SG core proteins exhibit heterogeneous distribution and distinct intrinsic features. Furthermore, we applied CAP-seq to map the RNA components in processing bodies (PBs) under both unstressed conditions and arsenite stimulation. By comparing the SG and PB transcriptomes, our data revealed that m6A modification may promote the localization of RNAs to SGs, while higher AU content may facilitate the targeting of mRNAs to PBs. This suggests potential regulatory roles in determining the subcellular localization of mRNAs within membrane-less organelles.
This dataset
Open GSE271045 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 GSE271045_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 PRJNA1129484 and SRA study SRP516809. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
12 conditions, mostly in duplicate
TIA1-miniSOG_HEK293T, arsenite-stress, label,… ×2 TIA1-miniSOG_HEK293T, arsenite-stress, label,… ×2 TIA1-miniSOG_HEK293T, arsenite-stress, omit p… ×2 G3BP2-miniSOG_HEK293T, arsenite-stress, label… ×2 G3BP2-miniSOG_HEK293T, arsenite-stress, label… ×2 G3BP2-miniSOG_HEK293T, arsenite-stress, omit … ×2 miniSOG-DDX6_HEK293T, unstressed, label, post… ×2 miniSOG-DDX6_HEK293T, unstressed, label, pre-… ×2 +4 more

Supports a between-group comparison across 24 samples.

How we read this: 12 replicated groups read from 24 sample titles; they account for 24 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.