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irCLIP-RNP reveals patterns of dynamic protein associations on RNA [RNA-seq]

GSE271168 Homo sapiens (human) RNA-seq (gene expression) 40 samples Submitted 2025/01/28 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 40 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
40 samples: 19 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
irCLIP-RNP and Re-CLIP reveal patterns of dynamic protein assemblies on RNANature · 2025
Summary (written by the submitters)
RNA binding proteins (RBPs) control varied processes, including RNA splicing, stability, transport, and translation. Dysfunctional RNA-RBP interactions contribute to the pathogenesis of human disease, however, characterizing the nature and dynamics of multiprotein assemblies on RNA has been challenging. To address this, non-isotopic ligation-based ultraviolet crosslinking immunoprecipitation was combined with mass spectrometry (irCLIP-RNP) to identify RNA-dependent associated proteins (RDAPs) co-bound to RNA with any RBP of interest.
Read the full summary ↓
irCLIP-RNP defined landscapes of multimeric protein assemblies on RNA, uncovering previously unknown patterns of RBP-RNA associations, including cell-type-selective combinatorial relationships between RDAPs and primary RBPs. irCLIP-RNP also defined dynamic RDAP remodeling in response to epidermal growth factor (EGF), uncovering EGF-induced recruitment of UPF1 adjacent to HNRNPC to effect splicing surveillance of cell proliferation mRNAs. To identify the RNAs simultaneously co-bound by multiple studied RBPs, a sequential immunoprecipitation irCLIP (Re-CLIP) method was also developed. Re-CLIP confirmed binding relationships seen in irCLIP-RNP and identified HNRNPC and UPF1 RBP co-binding on RND3 and DDX3X mRNAs. irCLIP-RNP and Re-CLIP provide a framework to identify and characterize dynamic RNA-protein assemblies in living cells.
Published in
irCLIP-RNP and Re-CLIP reveal patterns of dynamic protein assemblies on RNA
Ducoli L, Zarnegar BJ, Porter DF et al. · Nature 2025 · PMID 40140581 · doi:10.1038/s41586-025-08787-5
This dataset
Open GSE271168 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 GSE271168_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 PRJNA1130389 and SRA study SRP517210. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40140581) ↗
Study design
19 conditions, mostly in duplicate
siCSDE1, A431 , 1h EGF, ×2 siHNRNPC, A431 , 1h EGF, ×2 siUPF1, A431 , 1h EGF, ×2 Control siRNA, A431 , 1h EGF, 0h actinomycinD, ×2 siHNRNPC, A431 , 1h EGF, 0h actinomycinD, ×2 siUPF1, A431 , 1h EGF, 0h actinomycinD, ×2 Control siRNA, A431 , 1h EGF, A431 , 1h actin… ×2 siHNRNPC, A431 , 1h EGF, A431 , 1h actinomyci… ×2 +13 more

Supports a between-group comparison across 38 samples.

How we read this: 19 replicated groups read from 40 sample titles; they account for 38 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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