GEO series
In vivo systematic detection of the outcomes of CRISPR/Cas9 mediated DNA repair in skeletal muscle stem cells [sgRNA]
GSE303540
Mus musculus (mouse)
ChIP-seq / ATAC-seq (genome binding and open chromatin)
272 samples
Submitted 2026/04/23
Platform GPL24247Platform GPL34328Platform GPL18480
At a glance
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 272 samples
- What it is
- ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
- Organism
- Mus musculus (mouse)
- Samples
- 272 samples: 111 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
- 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
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
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.
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 GSE303540_RAW.tar (it can run to tens of gigabytes).
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.
What the files usually look like: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.
Also filed as BioProject PRJNA1284091 and SRA study SRP596456. Searching any of these in the dataset finder brings you back here.
Study design
111 conditions, mostly in duplicate
Lig4-KO ×9
Ctrl-for-Lig4 ×9
Ctrl-for-Ku80 ×8
Ku80-KO ×8
Ctrl-for-Nbn ×6
Nbn-KO ×6
Polq-KO ×5
Ctrl-for-Polq ×5
+107 more
Supports a between-group comparison across 268 samples.
How we read this: 111 replicated groups read from 272 sample titles; they account for 268 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
- GSM9129596 Single sgRNA target S1_rep1 Single sgRNA target S1
- GSM9129597 Single sgRNA target S1_rep2 Single sgRNA target S1
- GSM9129598 Single sgRNA target S2_rep1 Single sgRNA target S2
- GSM9129599 Single sgRNA target S2_rep2 Single sgRNA target S2
- GSM9129600 Single sgRNA target S3_rep1 Single sgRNA target S3
- GSM9129601 Single sgRNA target S3_rep2 Single sgRNA target S3
- GSM9129602 Single sgRNA target S4_rep1 Single sgRNA target S4
- GSM9129603 Single sgRNA target S4_rep2 Single sgRNA target S4
- GSM9129604 Single sgRNA target S5_rep1 Single sgRNA target S5
- GSM9129605 Single sgRNA target S5_rep2 Single sgRNA target S5
- GSM9129606 Single sgRNA target S6_rep1 Single sgRNA target S6
- GSM9129607 Single sgRNA target S6_rep2 Single sgRNA target S6
- GSM9129608 Single sgRNA target S7_rep1 Single sgRNA target S7
- GSM9129609 Single sgRNA target S7_rep2 Single sgRNA target S7
- GSM9129610 Single sgRNA target S8_rep1 Single sgRNA target S8
- GSM9129611 Single sgRNA target S8_rep2 Single sgRNA target S8
- GSM9129612 Single sgRNA target S9_rep1 Single sgRNA target S9
- GSM9129613 Single sgRNA target S9_rep2 Single sgRNA target S9
- GSM9129614 Single sgRNA target S10_rep1 Single sgRNA target S10
- GSM9129615 Single sgRNA target S10_rep2 Single sgRNA target S10
- GSM9129616 Single sgRNA target S11_rep1 Single sgRNA target S11
- GSM9129617 Single sgRNA target S11_rep2 Single sgRNA target S11
- GSM9129618 Single sgRNA target S13_rep1 Single sgRNA target S13
- GSM9129619 Single sgRNA target S13_rep2 Single sgRNA target S13
- GSM9129620 Single sgRNA target S14_rep1 Single sgRNA target S14
- GSM9129621 Single sgRNA target S14_rep2 Single sgRNA target S14
- GSM9129622 Single sgRNA target S15_rep1 Single sgRNA target S15
- GSM9129623 Single sgRNA target S15_rep2 Single sgRNA target S15
- GSM9129624 Single sgRNA target S16_rep1 Single sgRNA target S16
- GSM9129625 Single sgRNA target S16_rep2 Single sgRNA target S16
- GSM9129626 Single sgRNA target S17_rep1 Single sgRNA target S17
- GSM9129627 Single sgRNA target S17_rep2 Single sgRNA target S17
- GSM9129628 Single sgRNA target S18_rep1 Single sgRNA target S18
- GSM9129629 Single sgRNA target S18_rep2 Single sgRNA target S18
- GSM9129630 Single sgRNA target S19_rep1 Single sgRNA target S19
- GSM9129631 Single sgRNA target S19_rep2 Single sgRNA target S19
- GSM9129632 Single sgRNA target S20_rep1 Single sgRNA target S20
- GSM9129633 Single sgRNA target S20_rep2 Single sgRNA target S20
- GSM9129634 Single sgRNA target S21_rep1 Single sgRNA target S21
- GSM9129635 Single sgRNA target S21_rep2 Single sgRNA target S21
+ 232 more — browse all 272 samples with per-sample file links →
Datasets on a similar topic
- GSE327708 In vivo systematic detection of the outcomes of CRISPR/Cas9 mediated DNA repair in skeletal muscle stem cells 365 samples shares crispr, cas9, systematic, detection, outcomes, mediated, skeletal, repair
- GSE327391 In vivo systematic detection of the outcomes of CRISPR/Cas9 mediated DNA repair in skeletal muscle stem cells [control] 81 samples shares crispr, cas9, systematic, detection, outcomes, mediated, skeletal, repair
- GSE327392 In vivo systematic detection of the outcomes of CRISPR/Cas9 mediated DNA repair in skeletal muscle stem cells [IDM-Seq long-read] 12 samples shares crispr, cas9, systematic, detection, outcomes, mediated, skeletal, repair
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- GSE246545 CUT&Tag analysis of H3K4me3 and Paxip1 in CRISPR/Cas9-mediated Paxip1 knockout KPC1199 murine PDAC cell line 12 samples shares crispr, cas9, mediated
- GSE268045 StealTHY: enabling CRISPR-Cas9 screens in immunocompetent hosts to expose concealed metastatic regulators [paired-end] 70 samples shares crispr, cas9
- GSE268044 StealTHY: enabling CRISPR-Cas9 screens in immunocompetent hosts to expose concealed metastatic regulators [single-end] 45 samples shares crispr, cas9
- GSE324386 Transcriptomic profiling of CRISPR-Cas9 knockout of RAD51D, LIMCH1, and BRD9 in MC38 colorectal cancer cells reveals regulation of PD-L1 expression 29 samples shares crispr, cas9
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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.