Exploring Protein and Circuit Design Spaces Using Massively Parallel Microscopy-Based Screening

Abstract

We have developed a platform to characterize transcriptional circuit dynamics and protein bio- physics for hundreds of thousands or millions of variants in a single experiment using time-lapse microscopy. The platform comprises “mother machine” microfluidic devices that allow a million or more bacterial lineages to grow under uniform conditions, automated liquid handling to read out RNA-FISH barcodes for every cell in the device, long-read sequencing to link the RNA-FISH barcode to the variant sequence, a sequencing pipeline to accurately map each of the hundreds of thousands or millions of RNA-FISH barcodes to an error-free variant consensus sequence, and an image analysis pipeline to handle the terabytes of data and billions of imaged cells per experiment.