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Sequencing the genomes of individual cancer cells provides the highest resolution picture of intratumoral heterogeneity. To enable high throughput single cell DNAseq across thousands of individual cells per sample, we developed a droplet-based, automated partitioning technology for whole genome sequencing. We applied this approach on a set of gastric cancer cell lines and a primary gastric tumor. In parallel, we conducted a separate single cell RNAseq analysis on these same cancers and useddoi:10.1101/445932 fatcat:rfk67xvlmrfi7epcxhfhdmfxym