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Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection

GSE290248 Homo sapiens (human) RNA-seq (gene expression) 97 samples Submitted 2026/06/29 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 97 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
97 samples: 43 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
Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selectionMolecular cell · 2026
Summary (written by the submitters)
Alternative polyadenylation (APA) is a widespread mechanism of gene regulation that generates transcript isoforms with distinct 3' ends. While several RNA-binding proteins (RBPs) are known to regulate APA, the roles of the vast majority of RBPs in this process remain poorly characterized. Using a large scale tethered function assay, we screened a library of 879 human RBPs to identify regulators of APA.
Read the full summary ↓
We discovered 52 RBPs that modulate APA, validated their functions through knockdown PAS-seq and enhanced crosslinking and immunoprecipitation (eCLIP), and developed a fine-tuned transformer model to predict activators of PAS selection. We focused on two unexpected hits: GRB2, an adaptor protein with crucial roles in cell signaling, and RNPS1, a member of the exon junction complex (EJC). We uncovered mechanisms by which they modulate APA using affinity purification mass spectrometry (AP-MS) and biochemical assays. Our screennprovides a comprehensive resource of RBPs involved in APA and reveals unexpected roles of signaling factors in APA regulation.
Published in
Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection
Jagannatha P, Yoon Y, Landry SB et al. · Molecular cell 2026 · PMID 42361791 · doi:10.1016/j.molcel.2026.06.011
This dataset
Open GSE290248 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 GSE290248_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 PRJNA1226647 and SRA study SRP565555. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42361791) ↗
Study design
43 conditions, mostly in duplicate
non-target biol ×6 non-target 2 biol ×6 non-target 3 biol ×5 CPSF5 RNAi biol ×2 CPSF6 RNAi biol ×2 GRB2 RNAi biol ×2 RNPS1 RNAi biol ×2 RBM22 RNAi biol ×2 +35 more

Supports a between-group comparison across 97 samples.

How we read this: 43 replicated groups read from 97 sample titles; they account for 97 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

+ 57 more — browse all 97 samples with per-sample file links →

Datasets on a similar topic

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