Description of engineered cell lines used in this study.
Clonal cell lines derived from HAP1-7TGP in which a single or multiple genes were targeted using CRISPR/Cas9 are described in two separate spreadsheets labeled accordingly. When more than one clonal cell line was generated targeting the same gene or genes, the ‘Cell Line Name’ column indicates the generic name used throughout the manuscript to describe the genotype and the ‘Clone #' column identifies distinct individual clones. The figures in which each clone was used are also indicated. The ‘CRISPR guide’ column indicates the name of the guide used, which is the same as that of the oligonucleotides encoding sgRNAs (see Materials and methods and Supplementary file 3). The ‘Genomic Sequence’ column shows 80 nucleotides of genomic sequence (5’ relative to the gene is to the left) surrounding the target site; when two adjacent sites were targeted within the same gene, 80 nucleotides of genomic sequence surrounding each target site are shown and the number of intervening base pairs that are not shown between the two sites is indicated in parenthesis. Each group of clonal cell lines made using the same CRISPR guides is separated by a horizontal spacer and the ‘Genomic Sequence’ column is headlined by the reference WT genomic sequence (obtained from RefSeq). The guide sequence is colored blue and the site of the double strand cut made by Cas9 is between the two underlined bases. Sequencing results for individual clones are indicated below the reference sequence. Rare differences between the reference RefSeq sequence and the sequencing result obtained from HAP1-7TGP clones, as well as any undetermined sequences, are indicated in green. Some clones obtained following transfection with the indicated sgRNAs and single-cell sorting were found to be WT at the target site or sites; these are indicated as such and were used as controls. For mutant clones, mutated nucleotides are colored red (dashes represent deleted nucleotides, ellipses are used to indicate that a deletion continues beyond the 80 nucleotides of sequence shown and large insertions are indicated in brackets) and the nature of the mutation, the resulting genotype and any pertinent observations are also described. For clones in which multiple genes were targeted, the CRISPR guide (or pair of guides) used to target each gene as well as the genomic sequence, mutation, genotype and observations pertaining to each of the targeted genes are designated ‘1’, ‘2’, ‘3’ and so on in the column headings and are shown under horizontal spacers of different colors.