Pooled CRISPR screens with imaging on microRaft arrays reveals stress granule-regulatory factors

Here, we introduce CRaft-ID (CRISPR-based microRaft followed by gRNA identification) to enable the screening of image-based phenotypes such as subcellular protein localization from a pool of lenti-CRISPR bulk infected cells. Clonal colonies selected from microRaft arrays are isolated after phenotyping for a targeted-sequencing library preparation to identify the infected sgRNA in each colony. sgRNA representation in the pool of cells is measured with a targeted-sequencing library preparation from the bulk sample. Targeted-sequencing of sgRNA insert in the genome from a bulk sample of cells or individual microRaft cell colonies.