A one-week automated genome-wide optical pooled screen using OttoSeq

Optical pooled screens (OPS) are bottlenecked by labor-intensive in situ sequencing and analysis protocols. Here, we present OttoSeq, an automated OPS platform combining the Otto2 fluid handling system with the Brieflow analysis pipeline. We utilize OttoSeq to complete a genome-wide cell painting screen in eight days, sampling 5,198,240 high-quality cells across 21,732 gene knockout perturbations (224 cells per gene) and interpreting 320 functional gene clusters.