GEO series

QKI ensures splicing fidelity during cardiogenesis by engaging the U6 tri-snRNP to activate splicing at weak 5’splice sites [RNA-Seq]

GSE306690 Homo sapiens (human) Single-nucleus RNA-seq 30 samples Submitted 2025/09/17 Platform GPL16791Platform GPL34284

At a glance

Single-nucleus RNA-seq · human · 30 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: 30 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: QKI ensures splicing fidelity during cardiogenesis by engaging the U6 tri-snRNP to activate splicing at weak 5' splice sitesbioRxiv : the preprint server for biology · 2025

Summary (written by the submitters)

During organogenesis, the establishment of tissue architecture requires precise RNA processing. Many developmentally essential exons bear weak 5′ splice sites (5′SS) yet are spliced with high precision, implying unknown yet active splicing fidelity mechanisms. Combining transcriptome and alternative splicing profiling and with temporal eCLIP mapping of RNA interactions across development, we identify the RNA-binding protein QKI as an essential direct regulator of splicing fidelity in key cardiac transcripts.

Read the full summary ↓

Although QKI is dispensable for cardiac lineage specification, its loss disrupts sarcomere assembly despite intact expression of sarcomere mRNAs through exon skipping and intron retention in key sarcomeric mRNAs. QKI-dependent exons in essential cardiac genes have weak 5′SS and frequently show poor complementarity with U6 snRNA; we show that QKI directly interacts with U6 snRNA using an overlapping interface to its traditional intronic binding activity, securing U4/U6·U5 tri-snRNP recruitment to ensure exon inclusion. Thus, QKI exemplifies how context-aware RBPs enforce splicing fidelity at structurally vulnerable splice sites by coupling local intronic cues to spliceosome engagement, thereby securing accurate exon inclusion during organogenesis.

Published in

QKI ensures splicing fidelity during cardiogenesis by engaging the U6 tri-snRNP to activate splicing at weak 5' splice sites

Akinyi MV, Yao W, Zeman J et al. · bioRxiv : the preprint server for biology 2025 · PMID 40950209 · doi:10.1101/2025.09.04.674271

This dataset

Open GSE306690 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 GSE306690_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 PRJNA1311831 and SRA study SRP613847. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40950209) ↗

Study design

10 conditions, mostly in triplicate

D4-WT ×3 D4-KO ×3 D8-WT ×3 D8-KO ×3 D0-WT ×3 D0-KO ×3 D8_NuclearRNA_KO ×3 D8_NuclearRNA_WT ×3 +2 more

Supports a between-group comparison across 30 samples.

How we read this: 10 replicated groups read from 30 sample titles; they account for 30 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

GSM9206261 D4-WT-1 D4-WT
GSM9206262 D4-WT-2 D4-WT
GSM9206263 D4-WT-3 D4-WT
GSM9206264 D4-KO-1 D4-KO
GSM9206265 D4-KO-2 D4-KO
GSM9206266 D4-KO-3 D4-KO
GSM9206267 D8-WT-2 D8-WT
GSM9206268 D8-WT-3 D8-WT
GSM9206269 D8-WT-4 D8-WT
GSM9206270 D8-KO-1 D8-KO
GSM9206271 D8-KO-2 D8-KO
GSM9206272 D8-KO-4 D8-KO
GSM9206273 D0-WT-1 D0-WT
GSM9206274 D0-WT-2 D0-WT
GSM9206275 D0-WT-3 D0-WT
GSM9206276 D0-KO-1 D0-KO
GSM9206277 D0-KO-2 D0-KO
GSM9206278 D0-KO-3 D0-KO
GSM9206279 D8_NuclearRNA_KO_1 D8_NuclearRNA_KO
GSM9206280 D8_NuclearRNA_KO_2 D8_NuclearRNA_KO
GSM9206281 D8_NuclearRNA_KO_3 D8_NuclearRNA_KO
GSM9206282 D8_NuclearRNA_WT_1 D8_NuclearRNA_WT
GSM9206283 D8_NuclearRNA_WT_2 D8_NuclearRNA_WT
GSM9206284 D8_NuclearRNA_WT_3 D8_NuclearRNA_WT
GSM9206285 QKI_293T_siNC1 QKI_293T_siNC
GSM9206286 QKI_293T_siNC2 QKI_293T_siNC
GSM9206287 QKI_293T_siNC3 QKI_293T_siNC
GSM9206288 QKI_293T_siQKI1 QKI_293T_siQKI
GSM9206289 QKI_293T_siQKI2 QKI_293T_siQKI
GSM9206290 QKI_293T_siQKI3 QKI_293T_siQKI

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