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Fig. 6 | BMC Genomics

Fig. 6

From: Unsupervised correction of gene-independent cell responses to CRISPR-Cas9 targeting

Fig. 6

CRISPRcleanR enables detection of cancer gene dependencies. a Detection of EGFR and PIK3CA dependencies at the level of targeting sgRNAs in mutant cancer cell lines. Rank position of sgRNAs targeting the indicated genes before (top) and after (bottom) CRISPRcleanR correction. FE and non-essential genes are shown for comparison. b A CN-amplified region of chromosome 8 in HT-29 cell line including MYC and 3 surrounding up-streaming/down-streaming genes. Expanded view of sgRNAs targeting MYC and its surrounding genes, with each gene identified by a different colour. The heatmaps (first 7 columns) show ranked positions of the sgRNAs targeting the 7 considered genes (blue bars) before (top heatmap) and after (bottom heatmap) CRISPRcleanR correction. The last two columns show rank positions for the sgRNAs targeting FE genes (second last column) and non-essential genes (last column). c Same as for B but considering a region on chromosome 16 in the NCI-H2170 cell line, including ERBB2 and four flanking upstreaming/downstreaming genes and CDK12

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