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The RNA-binding protein PRRC2B preserves 5' TOP mRNA during starvation to maintain ribosome biogenesis during recovery

GSE282113 Homo sapiens (human) RNA-seq (gene expression) 15 samples Submitted 2025/10/26 Platform GPL34284
At a glance

RNA-seq (gene expression) · human · 15 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
15 samples: 4 × 293T cells, PRRC2B guides, DMEM, vs 4 × 293T cells, NT guide, EBSS 48hrs, vs 4 × 293T cells, PRRC2B guides, EBSS 48hrs, vs 3 × 293T cells, NT guide, DMEM,Groups 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
The RNA-binding protein PRRC2B preserves 5' TOP mRNA during starvation to maintain ribosome biogenesis during nutrient recoveryNucleic acids research · 2025
Summary (written by the submitters)
PRRC2B is an intrinsically disordered RNA-binding protein that is part of the cell’s translation machinery. Here we show that PRRC2B has two alternatively spliced mRNA transcripts producing major long and minor short isoforms. Mass spectrometry-based interaction studies indicated that both isoforms associate with the 40S ribosomal subunit and translation initiation factors.
Read the full summary ↓
Importantly, the long isoform also interacted with additional RNA-binding proteins through its unique Arg/Gly-rich region. Among these is LARP1, a regulator of 5' TOP mRNAs under conditions of mTOR inhibition. We discovered that like LARP1, PRRC2B is an important regulator of 5' TOP mRNA levels during starvation, particularly those encoding ribosomal proteins. Overall, our study elucidates a newly discovered function for PRRC2B as an RNA-binding protein that regulates ribosomal biogenesis, establishing it as a global regulator of translation in addition to its function in initiating specific target translation.
Published in
The RNA-binding protein PRRC2B preserves 5' TOP mRNA during starvation to maintain ribosome biogenesis during nutrient recovery
Goldberg N, Bril D, Eisenstein M et al. · Nucleic acids research 2025 · PMID 41385325 · doi:10.1093/nar/gkaf1334
This dataset
Open GSE282113 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 GSE282113_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 PRJNA1187217 and SRA study SRP545694. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41385325) ↗
Study design
4 × 293T cells, PRRC2B guides, DMEM, vs 4 × 293T cells, NT guide, EBSS 48hrs, vs 4 × 293T cells, PRRC2B guides, EBSS 48hrs, vs 3 × 293T cells, NT guide, DMEM,

Supports a between-group comparison across 15 samples.

How we read this: 4 replicated groups read from 15 sample titles; they account for 15 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
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