Active learning of enhancer and silencer regulatory grammar in photoreceptors
We performed iterative rounds of massively parallel reporter assay experiments in ex vivo retinas to generate training data for machine learning models of the photoreceptor cis-regulatory grammar. Overall design: A series of libraries of barcoded reporter gene plasmids were transfected into mouse retinas in triplicate. We measured barcoded reporter gene activity by RNA-seq, normalized by the DNA-seq reads of the input plasmid pool.