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RBProximity-CLIP enables subcellular mapping of RNA-binding protein interactions at nucleotide resolution [CLIP]

GSE311747 Homo sapiens (human) RNA-seq (gene expression) 27 samples Submitted 2026/01/12 Platform GPL18573Platform GPL30173
At a glance

RNA-seq (gene expression) · human · 27 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
27 samples: 10 conditions, mostly in triplicateGroups 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
RBProximity-CLIP Enables Subcellular Mapping of RNA-Binding Protein Interactions at Nucleotide ResolutionbioRxiv : the preprint server for biology · 2025
Summary (written by the submitters)
RNA-binding proteins (RBPs) orchestrate post-transcriptional gene regulatory (PTGR) processes through specific interactions with RNA molecules, which are tightly regulated in both space and time, including through the subcellular compartmentalization of RBPs and their target RNAs.
Read the full summary ↓
To characterize these interactions in specific subcellular compartments, we developed RBProximity-CLIP, an approach that integrates targeted APEX2-based proximity labeling with 4-thiouridine–enhanced RNA–protein crosslinking to enable the isolation and profiling of target sites of individual RBPs in a compartment-specific manner . Using this approach, we profiled three RBPs—AGO2, YBX1, and ELAVL1—within the cytoplasmic, nuclear, and nucleolar compartments. RBProximity-CLIP enabled robust isolation of compartment specific RBP-RNA interactome and new insights of compartmental specific gene regulation of distinct RBPs.
Published in
RBProximity-CLIP Enables Subcellular Mapping of RNA-Binding Protein Interactions at Nucleotide Resolution
Nowak I, Polash AH, Huynh HT et al. · bioRxiv : the preprint server for biology 2025 · PMID 41473311 · doi:10.64898/2025.12.12.693770
This dataset
Open GSE311747 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 GSE311747_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 PRJNA1370860 and SRA study SRP649680. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41473311) ↗
Study design
10 conditions, mostly in triplicate
HEK293 APEX2 ELAVL1 nucleolar lysate ×3 HEK293 total lysate for ELAVL1 ×3 HEK293 APEX2 YBX1 nuclear lysate biol ×3 HEK293 APEX2 YBX1 cytoplasmic lysate biol ×3 HEK293 APEX2 YBX1 nucleolar lysate biol ×3 HEK293 total lysate for YBX1 ×3 HEK293 APEX2 AGO2 nuclear lysate biol ×2 HEK293 APEX2 AGO2 cytoplasmic lysate biol ×2 +3 more

Supports a between-group comparison across 26 samples.

How we read this: 10 replicated groups read from 27 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
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