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The U1 snRNP protein U1C and Helix H of U1 snRNA are critical for small molecule splicing modulator function

GSE304951 Homo sapiens (human) Single-nucleus RNA-seq 57 samples Submitted 2026/07/24 Platform GPL34284
At a glance

Single-nucleus RNA-seq · human · 57 samples

What it is
Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue).
Organism
Homo sapiens (human)
Samples
57 samples: 23 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
The U1 snRNP protein U1C and Helix H of U1 snRNA are critical for small molecule splicing modulator functionNature communications · 2026
Summary (written by the submitters)
Risdiplam and branaplam are two small molecule splicing modulators that enhance the ability of U1 snRNP to recognize non-canonical GA/GU-containing 5’ splice sites (ss). We demonstrated that branaplam improves the recognition of these 5’ ss by reconstituted U1 snRNP in vitro and that this effect is dependent on the ZnF domain of U1C and Helix H of U1 snRNA but not U1A or U1-70K.
Read the full summary ↓
We then showed in vivo depletion of U1C decreases the potency of most compound-induced cassette exons. However, many cassette exons only become responsive to compound when U1C is depleted, leading to a model where U1C stabilizes different context-dependent structural conformations of U1 snRNP which either promotes or hinders compound binding and its effect on splicing. Surprisingly, risdiplam has no effect on the recognition of these 5’ ss in vitro, suggesting additional cellular factors are required.
Published in
The U1 snRNP protein U1C and Helix H of U1 snRNA are critical for small molecule splicing modulator function
Kuang Z, Kosmyna B, Li X et al. · Nature communications 2026 · PMID 42463664 · doi:10.1038/s41467-026-74765-8
This dataset
Open GSE304951 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 GSE304951_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1303585 and SRA study SRP607627. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42463664) ↗
Study design
23 conditions, mostly in duplicate
control siRNA, + DMSO, ×4 U1C siRNA, + DMSO, ×4 mock, ×4 control siRNA, + risdiplam 1.2uM, ×2 control siRNA, + risdiplam 200nM, ×2 control siRNA, + risdiplam 3.6uM, ×2 control siRNA, + risdiplam 400nM, ×2 control siRNA, + risdiplam 50nM, ×2 +20 more

Supports a between-group comparison across 52 samples.

How we read this: 23 replicated groups read from 57 sample titles; they account for 52 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

+ 17 more — browse all 57 samples with per-sample file links →

Datasets on a similar topic

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