References
Guide library sources
- Doench JG et al. Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nature Biotechnology (2016). DOI: 10.1038/nbt.3437. PMID: 26780180.
- Sanson KR et al. Optimized libraries for CRISPR-Cas9 genetic screens with multiple modalities. Nature Communications (2018). DOI: 10.1038/s41467-018-07901-8. PMID: 30575746.
Cloning and backbone sources
- Sanjana NE, Shalem O and Zhang F. Improved vectors and genome-wide libraries for CRISPR screening. Nature Methods (2014). DOI: 10.1038/nmeth.3047. PMID: 25075903.
- Joung J et al. Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening. Nature Protocols (2017). DOI: 10.1038/nprot.2017.016. PMID: 28333914.
- Vector records: lentiGuide-Puro (Addgene #52963); lentiCRISPR v2 (Addgene #52961).
- Packaging plasmids: psPAX2 (Addgene #12260); pMD2.G (Addgene #12259).
Primary analysis software
- Li W et al. MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens. Genome Biology (2014). DOI: 10.1186/s13059-014-0554-4. PMID: 25476604.
Prime Editing MAVE sources
- Anzalone AV et al. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature (2019). DOI: 10.1038/s41586-019-1711-4. PMID: 31634902.
- Mathis N et al. Machine learning prediction of prime editing efficiency across diverse chromatin contexts (PRIDICT2.0). Nature Biotechnology (2025; online 2024). DOI: 10.1038/s41587-024-02268-2. PMID: 38907037.
- Nelson JW et al. Engineered pegRNAs improve prime editing efficiency (pegLIT). Nature Biotechnology (2022). DOI: 10.1038/s41587-021-01039-7. PMID: 34608327.
- Cirincione A et al. A benchmarked, high-efficiency prime editing platform for multiplexed dropout screening. Nature Methods (2025). DOI: 10.1038/s41592-024-02502-4. PMID: 39562753.
- Non-targeting control source: StopPR epegRNA pooled library (Addgene #227706).
- PE vector: sgOpti-tevoPQ1 (Addgene #255532). Associated publication: Martyn GE et al. Rewriting regulatory DNA to dissect and reprogram gene expression. Cell (2025). DOI: 10.1016/j.cell.2025.03.034. PMID: 40245860.