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Development of a split-toxin CRISPR screening platform to systematically identify upstream regulators of human myoblast fusion

GSE293514 Homo sapiens (human) Single-cell RNA-seq 57 samples Submitted 2025/10/24 Platform GPL34281Platform GPL29480
At a glance

Single-cell RNA-seq · human · 57 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. 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
57 samples: 28 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
Development of a split-toxin CRISPR screening platform to systematically identify regulators of human myoblast fusionNature communications · 2026
Summary (written by the submitters)
Muscle defects are a common feature in human developmental disorders and often lead to severe functional impairment. These defects arise from intricate tissue crosstalk and rare genetic mutations, underscoring the need to systematically identify cell-autonomous mechanisms regulating human myogenesis. Despite the clinical significance, our understanding of human development remains limited, due in part to the absence of a scalable genetic approach to study this process.
Read the full summary ↓
Here, we introduce a rationally designed high-throughput CRISPR screening platform that integrates human myoblast models, muscle-specific CRISPR knockout libraries, and a split-toxin strategy that acts as a functional readout for myoblast fusion—a fundamental step of human myogenesis. This screening strategy enables selection of CRISPR-induced fusion-defective myocytes in a quantifiable manner. Leveraging this platform, our initial genetic screen uncovered a large group of new hits essential for human myoblast fusion. The majority of these hits converge into 23 protein complexes, most of which have not previously been functionally linked to myogenesis in any species. Notably, mutations in 41 of our fusion screen hits cause human diseases presenting abnormal skeletal muscle morphology. Applying a new single-cell CRISPR & RNA-seq approach, we show that majority of these hits control human myoblast fusion as well as influence early-stage myogenic differentiation. Together, this work presents a new systematic approach to study human myogenesis and uncovers promising candidates governing human muscle differentiation and fusion. A broader application of this split-toxin based CRISPR screening platform would accelerate the study of cell-autonomous mechanisms of human muscle development and diseases at scale.
Published in
Development of a split-toxin CRISPR screening platform to systematically identify regulators of human myoblast fusion
Zhang H, Shang R, Zhang Z et al. · Nature communications 2026 · PMID 41540035 · doi:10.1038/s41467-025-67583-x
This dataset
Open GSE293514 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 GSE293514_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 PRJNA1244860 and SRA study SRP575766. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41540035) ↗
Study design
28 conditions, mostly in duplicate
A1 human myoblast, GM, repeat ×2 A1 human myoblast, DM2d, repeat ×2 A1 human myoblast, DM6d, repeat ×2 A16 human myoblast, GM, repeat ×2 A16 human myoblast, DM2d, repeat ×2 A16 human myoblast, DM6d, repeat ×2 A15 human myoblast, GM, repeat ×2 A15 human myoblast, DM2d, repeat ×2 +21 more

Supports a between-group comparison across 56 samples.

How we read this: 28 replicated groups read from 57 sample titles; they account for 56 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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