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Transcriptome-wide mapping of RNA:protein interactions of PRPF8 and SNRNP200 (BRR2) with retinitis pigmentosa (RP) mutations by iCLIP

GSE213806 Homo sapiens (human) Single-nucleus RNA-seq 27 samples Submitted 2025/03/12 Platform GPL11154
At a glance

Single-nucleus RNA-seq · human · 27 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). Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Homo sapiens (human)
Samples
27 samples: 27 samples, each with a distinct title — no replicated groupsGroups 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
Retinitis pigmentosa-linked mutations impair the snRNA unwinding activity of SNRNP200 and reduce pre-mRNA binding of PRPF8Cellular and molecular life sciences : CMLS · 2025
Summary (written by the submitters)
We used HeLa cells that express GFP-tagged PRPF8 with and without the RP mutations F2314L and Y2334N at physiological levels as well as SNRNP200-GFP with and without the RP mutations S1087L and R1090L and performed iCLIP using anti-GFP antibodies. We also used RPE cells with and without the Y2334N mutation inserted by CRISPR/Cas9 and compared their binding pattern on snRNAs and pre-mRNAs.
Published in
Retinitis pigmentosa-linked mutations impair the snRNA unwinding activity of SNRNP200 and reduce pre-mRNA binding of PRPF8
Zimmann F, McNicoll F, Thakur PK et al. · Cellular and molecular life sciences : CMLS 2025 · PMID 40045025 · doi:10.1007/s00018-025-05621-z
This dataset
Open GSE213806 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 GSE213806_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 PRJNA882472 and SRA study SRP398282. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40045025) ↗
Study design
27 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 27 sample titles: 27 distinct titles with little repetition. 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
Datasets on a similar topic

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.