GEO series

In vivo systematic detection of the outcomes of CRISPR/Cas9 mediated DNA repair in skeletal muscle stem cells [IDM-Seq long-read]

GSE327392 Mus musculus (mouse) Other 12 samples Submitted 2026/04/23 Platform GPL24973

At a glance

mouse · 12 samples

Organism: Mus musculus (mouse)
Samples: 12 samples: 2 × long-read S1 vs 2 × long-read S7 vs 2 × long-read S18 vs 2 × long-read S28Groups 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.
Paper: In vivo systematic detection of the outcomes of CRISPR-Cas9-mediated DNA repair in skeletal muscle stem cellsMolecular therapy : the journal of the American Society of Gene Therapy · 2026

Summary (written by the submitters)

CRISPR/Cas9 has revolutionized genome editing with broad therapeutic applications, yet its repair patterns in vivo remain poorly understood. Here, we systematically profile CRISPR/Cas9 editing outcomes at 95 loci using our established CRISPR/Cas9/AAV9-sgRNA system in skeletal muscle stem cells (MuSCs). Through comprehensive characterization of the repair outcomes, our findings demonstrate that the general rules governing CRISPR/Cas9-mediated editing in vivo largely align with those observed in vitro.

Read the full summary ↓

Additional to the anticipated small editing indels such as MMEJ mediated deletions and NHEJ mediated templated insertions, we uncover a prevalent occurrence of large on-target modifications, including large deletions (LDs) characterized by microhomology (MH) and large insertions (LIs). Notably, the LIs comprise not only exogenous AAV vector integrations but also endogenous genomic DNA fragments (Endo-LIs). Endo-LIs preferentially originate from active genomic regions, with their integration shaped by three-dimensional chromatin architecture. By disrupting key components of the NHEJ and MMEJ repair pathways in vivo, we identify their distinct roles in regulating the large on-target modifications. Together, our work systematically profiles the CRISPR/Cas9 repair outcomes in vivo and offers valuable guidance for improving the safety of CRISPR/Cas9-based gene therapies.

Published in

In vivo systematic detection of the outcomes of CRISPR-Cas9-mediated DNA repair in skeletal muscle stem cells

He L, Fu Y, Wang Z et al. · Molecular therapy : the journal of the American Society of Gene Therapy 2026 · PMID 42015511 · doi:10.1016/j.ymthe.2026.04.032

This dataset

Open GSE327392 in finder → Find more mouse datasets →

Download · which file do I need?

Direct links to NCBI, 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.

All supplementary files ↗

3 · The original raw files

Whole study · RAW.tar

Everything the authors deposited as one archive (GSE327392_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.

Whole study · RAW.tar ↓

Also filed as BioProject PRJNA1284091. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42015511) ↗

Study design

2 × long-read S1 vs 2 × long-read S7 vs 2 × long-read S18 vs 2 × long-read S28

Supports a between-group comparison across 8 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 8 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

GSM9656196 long-read S1_repwt
GSM9656197 long-read S1_rep1 long-read S1
GSM9656198 long-read S1_rep2 long-read S1
GSM9656199 long-read S7_repwt
GSM9656200 long-read S7_rep1 long-read S7
GSM9656201 long-read S7_rep2 long-read S7
GSM9656202 long-read S18_repwt
GSM9656203 long-read S18_rep1 long-read S18
GSM9656204 long-read S18_rep2 long-read S18
GSM9656205 long-read S28_repwt
GSM9656206 long-read S28_rep1 long-read S28
GSM9656207 long-read S28_rep2 long-read S28

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