Fig. 1

Genome-wide CRISPR knockout screens in PEL cell lines. a Experimental outline. Cas9-expressing cell pools or clones were infected with the lentiviral GeCKO v2 or Brunello sgRNA libraries. After complete puromycin selection, cells were split every 2–3 days and maintained at 500× sgRNA coverage. After 14–18 days, sgRNA composition was analyzed by Illumina sequencing and MAGeCK. b Cell lines and conditions used in this study. c Numbers of genes with significantly depleted sgRNAs in each screen (adj. p value < 0.05). “G” indicates cells were screened with GeCKO v2 library; all others were screened with Brunello. Cyan: EBV(+) PEL cells; blue: EBV(−) PEL cells; red: multiple myeloma; purple: Burkitt’s lymphoma. d Representative gene set enrichment analysis (GSEA) from BCBL-1 Cas9 clone screened using Brunello library. Genes were ranked by sgRNA depletion scores, with genes with depleted sgRNAs at the right end of the x-axis. NES normalized enrichment score, FDRq FDR-adjusted p value. e Heatmap of GSEA NESs of housekeeping pathways (Reactome) in all PEL cell lines (see Supplementary Data 7). Screens designated “G” used GeCKO v2 library. f Principal component analysis of normalized sgRNA reads from EBV(−) (blue shades) or EBV(+) PEL cells (red shades). sgRNAs from genes that have adj. p < 0.05 in at least one cell line were examined. Only data from Brunello screens were considered