We then applied these methods to execute 3 whole genome (80,862 sgRNAs targeting 20,393 genes) CRISPR KO screens in A549, and HeLa (paired screens with different growth media).
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These screens generated rich phenotypic data, enabling us to use morphological profile similarity to explore relationships between perturbed genes such as clustering protein complex members by morphological similarity, and capturing membership/directionality of signaling pathways.
We were also able to use this clustering-by-morphological similarity information (plus mechanistic follow-up) to identify a role for the poorly characterized gene TMEM251 in lysosomal protein trafficking through the M6P-system.
In sum, pooled optical screens are a powerful approach for generating high-dimensional genotype-phenotype maps, and we demonstrate that these maps can now be generated routinely (and at a low cost per cell profile) at genome scale using standard imaging equipment and open source analysis pipelines.
We believe this combination of accessibility and cost effectiveness make PERISCOPE-style screens a democratizing platform technology for linking genotypes to cellular programs.
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