ArticleSTAR protocols2022
PEM-seq comprehensively quantifies DNA repair outcomes during gene-editing and DSB repair.
Article in STAR protocols, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
32 citing papers in PubMed.
- Article
- Decoding DNA metabolism and its clinical relevance through the lens of high-throughput sequencing assays.Medical review (2021) · 2026Review
- Prime Editing Exhibits Limited Genome-Wide Off-Target Effects in Cellular and Embryonic Gene Editing.Cells · 2026Article
- Comprehensive assessment of activity, specificity, and safety of hypercompact TnpB systems for gene editing.Genome biology · 2026Article
- Structural and functional bases of F. rodentium Cas9 provide insights into CRISPR-Cas protein engineering.Cell genomics · 2026Article
- Targeting transthyretin by one Cas9 variant with superfidelity and broad compatibility.Science advances · 2026Article
- HTGTS-TCR-Seq for Profiling of Mouse and Human T-Cell Receptor α and β Gene Rearrangements and Diversity.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Engineering eukaryotic transposon-encoded Fanzor2 system for genome editing in mammals.Nature chemical biology · 2026Article
- Off-target effects in CRISPR-Cas genome editing for human therapeutics: Progress and challenges.Molecular therapy. Nucleic acids · 2025Review
- Engineered Un1Cas12f1 with boosted gene-editing activity and expanded genomic coverage.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Deep Learning Based Models for CRISPR/Cas Off-Target Prediction.Small methods · 2025Review
- Systematic high-throughput evaluation reveals FrCas9's superior specificity and efficiency for therapeutic genome editing.Science advances · 2025Article
- Engineered IscB-ωRNA system with expanded target range for base editing.Nature chemical biology · 2025Article
- Adenine base editors induce off-target structure variations in mouse embryos and primary human T cells.Genome biology · 2024Article
- Transfer of mitochondrial DNA into the nuclear genome during induced DNA breaks.Nature communications · 2024Article
- On- and off-target effects of paired CRISPR-Cas nickase in primary human cells.Molecular therapy : the journal of the American Society of Gene Therapy · 2024Article
- Developmental progression of DNA double-strand break repair deciphered by a single-allele resolution mutation classifier.Nature communications · 2024Article
- DNA Damage Atlas: an atlas of DNA damage and repair.Nucleic acids research · 2024Article
- Generating universal anti-CD19 CAR T cells with a defined memory phenotype by CRISPR/Cas9 editing and safety evaluation of the transcriptome.Frontiers in immunology · 2024Article
- Cohesin maintains replication timing to suppress DNA damage on cancer genes.Nature genetics · 2023Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The repair products of double-stranded DNA breaks (DSBs) are crucial for investigating the mechanism underlying DNA damage repair as well as evaluating the safety and efficiency of gene-editing; however, a comprehensively quantitative assay remains to be established. Here, we describe the step-by-step instructions of the primer extension-mediated sequencing (PEM-seq), followed by the framework of data processing and statistical analysis. PEM-seq presents a full spectrum of repair outcomes for both genome-editing-induced and endogenous DSBs in mouse and human cells. For complete details on the use and execution of this profile, please refer to Gan et al. (2021), Yin et al. (2019), Liu et al. (2021a), and Zhang et al. (2021).
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Registered trials
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