Rapid generation of homozygous fluorescent knock-in human cells using CRISPR–Cas9 genome editing and validation by automated imaging and digital PCR screening

Cai, Y. et al. Experimental and computational framework for a dynamic protein atlas of human cell division. Nature 561, 411–415 (2018).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Walther, N. et al. A quantitative map of human Condensins provides new insights into mitotic chromosome architecture. J. Cell Biol. 217, 2309–2328 (2018).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wutz, G. et al. Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins. EMBO J. 36, 3573–3599 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cattoglio, C. et al. Determining cellular CTCF and cohesin abundances to constrain 3D genome models. eLife 8, e40164 (2019).

Article  PubMed  PubMed Central  Google Scholar 

Koch, B. et al. Generation and validation of homozygous fluorescent knock-in cells using CRISPR–Cas9 genome editing. Nat. Protoc. 13, 1465–1487 (2018).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Otsuka, S. et al. A quantitative map of nuclear pore assembly reveals two distinct mechanisms. Nature 613, 575–581 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Aksenova, V., Arnaoutov, A. & Dasso, M. Analysis of nucleoporin function using inducible degron techniques. Meth. Mol. Biol. https://doi.org/10.1007/978-1-0716-2337-4_9 (2022).

Article  Google Scholar 

Yang, Y. et al. A dual AAV system enables the Cas9-mediated correction of a metabolic liver disease in newborn mice. Nat. Biotechnol. 34, 334–338 (2016).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gao, X. et al. Treatment of autosomal dominant hearing loss by in vivo delivery of genome editing agents. Nature 553, 217–221 (2018).

Article  CAS  PubMed  Google Scholar 

Santiago-Fernández, O. et al. Development of a CRISPR/Cas9-based therapy for Hutchinson–Gilford progeria syndrome. Nat. Med. 25, 423–426 (2019).

Article  PubMed  PubMed Central  Google Scholar 

Chen, S. et al. CRISPR-READI: efficient generation of knockin mice by CRISPR RNP electroporation and AAV donor infection. Cell Rep. 27, 3780–3789.e4 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kunzelmann, S., Böttcher, R., Schmidts, I. & Förstemann, K. A comprehensive toolbox for genome editing in cultured Drosophila melanogaster cells. G3 6, 1777–1785 (2016).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Paix, A. et al. Scalable and versatile genome editing using linear DNAs with microhomology to Cas9 sites in Caenorhabditis elegans. Genetics 198, 1347–1356 (2014).

Article  PubMed  PubMed Central  Google Scholar 

Schwartz, M. L. & Jorgensen, E. M. SapTrap, a toolkit for high-throughput CRISPR/Cas9 gene modification in Caenorhabditis elegans. Genetics 202, 1277–1288 (2016).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Okamoto, S., Amaishi, Y., Maki, I., Enoki, T. & Mineno, J. Highly efficient genome editing for single-base substitutions using optimized ssODNs with Cas9-RNPs. Sci. Rep. 9, 4811 (2019).

Article  PubMed  PubMed Central  Google Scholar 

Liang, X., Potter, J., Kumar, S., Ravinder, N. & Chesnut, J. D. Enhanced CRISPR/Cas9-mediated precise genome editing by improved design and delivery of gRNA, Cas9 nuclease, and donor DNA. J. Biotechnol. 241, 136–146 (2017).

Article  CAS  PubMed  Google Scholar 

Roth, T. L. et al. Reprogramming human T cell function and specificity with non-viral genome targeting. Nature 559, 405–409 (2018).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kim, S., Kim, D., Cho, S. W., Kim, J. & Kim, J. S. Highly efficient RNA-guided genome editing in human cells via delivery of purified Cas9 ribonucleoproteins. Genome Res. 24, 1012–1019 (2014).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Naeem, M., Majeed, S., Hoque, M. Z. & Ahmad, I. Latest developed strategies to minimize the off-target effects in CRISPR–Cas-mediated genome editing. Cells 9, 1608 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hanlon, K. S. et al. High levels of AAV vector integration into CRISPR-induced DNA breaks. Nat. Commun. 10, 4439 (2019).

Article  PubMed  PubMed Central  Google Scholar 

Schiel, J. A., Gross, M., Chou, E. T. & Kelley, M. Fluorescent tagging of an endogenous gene by homology-directed repair using Dharmacon TM Edit-R TM CRISPR-Cas 9 reagents. https://api.semanticscholar.org/CorpusID:22921699 (Dharmacon Life Sciences, 2016).

Paix, A., Rasoloson, D., Folkmann, A. & Seydoux, G. Rapid tagging of human proteins with fluorescent reporters by genome engineering using double-stranded DNA donors. Curr. Protoc. Mol. Biol. 129, e102 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Taylor, S. C., Laperriere, G. & Germain, H. Droplet digital PCR versus qPCR for gene expression analysis with low abundant targets: from variable nonsense to publication quality data. Sci. Rep. 7, 2409 (2017).

Article  PubMed  PubMed Central  Google Scholar 

Witte, A. K. et al. A systematic investigation of parameters influencing droplet rain in the Listeria monocytogenes prfA assay-reduction of ambiguous results in ddPCR. PLoS ONE 11, e0168179 (2016).

Article  PubMed  PubMed Central  Google Scholar 

Krumbholz, M. et al. Large amplicon droplet digital PCR for DNA-based monitoring of pediatric chronic myeloid leukaemia. J. Cell Mol. Med. 23, 4955–4961 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Madic, J. et al. Three-color crystal digital PCR. Biomol. Detect Quantif. 10, 34–46 (2016).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Engler, C., Kandzia, R. & Marillonnet, S. A one pot, one step, precision cloning method with high throughput capability. PLoS ONE 3, e3647 (2008).

Article  PubMed  PubMed Central  Google Scholar 

Doudna, J. A. & Sontheimer, E. J. Methods in enzymology. The use of CRISPR/Cas9, ZFNs, and TALENs in generating site-specific genome alterations. Preface. Methods Enzymol. 546, 19–20 (2014).

Google Scholar 

Liang, X. et al. Rapid and highly efficient mammalian cell engineering via Cas9 protein transfection. J. Biotechnol. 208, 44–53 (2015).

Article  CAS  PubMed  Google Scholar 

Hendel, A. et al. Chemically modified guide RNAs enhance CRISPR–Cas genome editing in human primary cells. Nat. Biotechnol. 33, 985–989 (2015).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Monia, B. P., Johnston, J. F., Sasmor, H. & Cummins, L. L. Nuclease resistance and antisense activity of modified oligonucleotides targeted to

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