Overview of the STARR-seq pipeline. First a reporter library is cloned from an arbitrary DNA source, which can be sonicated genomic DNA for comprehensive genome-wide screens. The reporter library is transfected into cultured cells and the reporter transcripts are isolated from the pool of total RNA after 24 h. After cDNA synthesis and PCR amplification of the self-transcribing sequences, deep sequencing is conducted and the resulting reads are mapped to the reference genome. The enrichment of reporter cDNA over input directly and quantitatively reflects enhancer activity.