Amplicon sequencing of edited OpenCell alleles

Amplicon sequencing of edited alleles from the OpenCell project. In this project, a split-mNeonGreen tag sequence (90nt) is inserted via CRISPR-based HDR (homology-directed repair) into protein-coding genes in HEK293T cells (see PMID 35271311 for more info. ). Here we used amplicon sequencing (paired-end MiSeq 2x300) to genotype the sequence landscape of each CRISPR-edited allele and quantify NHEJ (non-homologous end-joining) and HDR rates. Sequences were amplified from genomic DNA from a polyclonal pool of > 10,000 CRISPR-edited cells in each sample. No selection was used to enrich for edited cells ("unsorted" cells) in order to measure global HDR rates post-editing.