Extended Data Fig. 5: Analysis of CPD co-essential module with a 145 × 145 gene genetic-interaction map.

a, Cloning of CDKO library. A total of 463 sgRNAs targeting 145 hits from the 3D/2D phenotypes were PCR-amplified from an oligonucleotide array. These 145 hits include members of the CPD co-essential module. sgRNAs were separately cloned into two lentiviral vectors with either a mU6 or a hU6 promoter to generate two CRISPR single-knockout libraries. hU6-sgRNA cassettes were then cut out from one library and ligated into the other library containing the mU6 promoter. This generated a CDKO library with all possible pairwise combinations of the 463 sgRNAs (214,369 double sgRNAs). This CDKO library was used to measure genetic interactions (GIs) of 10,440 gene pairs (145 × 145 combinations). b, The 145 × 145 genetic-interaction map; the 145 × 145 matrix of genetic-interaction scores are shown as a heat map. The 145 genes are clustered by the similarities of their genetic interactions (Pearson correlation coefficients of genetic interactions) in the map. Members of the CPD co-essential module form a cluster (marked with red box) in this genetic-interaction map, consistent with their correlations in the DepMap CRISPR dataset. c, A genetic-interaction map validates the CPD co-essential module in H23. Correlations of genetic interactions are used to sort 145 genes on the basis of their similarities to genetic interactions of CPD. Genes in the CPD module are marked with red dots along the sorted genes.