CRISPR/Cas9-engineered clonal cell lines used in this study.

Single-mutant clones in which a single gene was targeted using CRISPR/Cas9 and double- or triple-mutant clones in which multiple genes were targeted using CRISPR/Cas9 are described in two separate spreadsheets labeled accordingly. When more than one clone was generated using the same CRISPR guide, the ‘Clone Name’ column indicates the generic name used throughout the manuscript to describe the genotype, and the ‘Clone #’ column identifies an individual clone. The ‘HDR Donor’ column indicates the name of the ssODN donor template used to generate some of the clonal cell lines (see Materials and methods). The ‘CRISPR guide’ column indicates the name of the guide used, which is the same as that of the oligos encoding sgRNAs (see Materials and methods, and S2 File). The ‘Genomic Sequence’ column shows 80 bases of genomic sequence (5’ relative to the gene is to the left) surrounding the target site. For each group of clones made using the same CRISPR guide (separated by gray spacers), the ‘Genomic Sequence’ column is headlined by the reference WT genomic sequence (obtained from RefSeq), with the guide sequence colored blue. 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. Some clones that remained WT at the targeted locus are indicated as such and were used as controls. For mutant clones, mutated bases are colored red (dashes represent deleted bases, three dots are used to indicate that a deletion continues beyond the 80 bases of sequence shown, and large insertions are indicated in brackets), and the nature of the mutation and the resulting genotype are described in the columns labeled accordingly. The figures in which each clone was used are also indicated. For double- and triple-mutant clones, the CRISPR guide used, the genomic sequence, the mutation and the genotype pertaining to each of the two or three targeted loci are designated ‘1’, ‘2’ and ‘3’ in the column headings, and are shown under green, orange and purple spacers, respectively. (XLSX)