← BioTransfer GEO Dataset Finder
GEO series

Systematic characterization of the composition and dynamics of processing body-associated mRNAs [dataset 2]

GSE279284 Homo sapiens (human) RNA-seq (gene expression) 131 samples Submitted 2025/09/15 Platform GPL24676Platform GPL34284Platform GPL24106
At a glance

RNA-seq (gene expression) · human · 131 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
131 samples: 59 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
Systematic characterization of the composition and dynamics of processing body-associated mRNAsNature communications · 2025
Summary (written by the submitters)
Processing bodies (PBs) are dynamic, membraneless organelles consisting of RNAs and proteins. While PB proteins have been extensively characterized, the methods for systematically profiling PB-associated RNAs are limited. To address this, we developed PB-TRIBE-STAMP, a new tool based on two orthogonal RNA editing enzymes. Simultaneously applying APOBEC1-DDX6 and LSM14A-ADAR2dd, PB-TRIBE-STAMP identified 1,639 and 2,577 PB-associated mRNAs in HCT116 and HEK293T cells, respectively.
Read the full summary ↓
Further genetic perturbation demonstrated that these transcripts were translationally repressed by PBs. Next, integration of PB-TRIBE-STAMP with long-read sequencing revealed that the PB-associated transcripts possessed shorter poly(A)-tails. Moreover, we established a TRIBE-ID-based tool to characterize the mRNA-PB association at high temporal resolution and unveiled a higher splicing efficiency of PB-associated XBP1 transcripts during unfolded protein response (UPR). Finally, based on sc-LSM14A-TRIBE-ID, we demonstrated the dynamic pattern of mRNA-PB interaction during cell cycle progression.
Published in
Systematic characterization of the composition and dynamics of processing body-associated mRNAs
Sun Z, Wen X, Li Y et al. · Nature communications 2025 · PMID 41213943 · doi:10.1038/s41467-025-64848-3
This dataset
Open GSE279284 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 GSE279284_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 PRJNA1171810 and SRA study SRP537962. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41213943) ↗
Study design
59 conditions, mostly in duplicate
HCT116_induced_APOBEC1-control ×3 HCT116_induced_APOBEC1-DDX6 ×3 HCT116_uninduced_APOBEC1-control ×3 HCT116_uninduced_APOBEC1-DDX6 ×3 HCT116_DDX6-KO_polysome ×2 HCT116_DDX6-KO_total ×2 HCT116_induced_4E-T-ADAR2dd ×2 HCT116_induced_4E-T-APOBEC1 ×2 +60 more

Supports a case/control comparison: 61 samples read as cases, 8 as controls.

How we read this: 59 replicated groups read from 131 sample titles; they account for 122 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

+ 91 more — browse all 131 samples with per-sample file links →

Datasets on a similar topic

Search all human RNA-seq datasets in GEO →

Share this dataset

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.