library_construction_protocol: STARR-seq: We extracted RNA using 3 RNAeasy columns per 25-million cells and isolated polyA+ mRNA using the Qiagen Oligotex mRNA kit.  Motif-modification STARR-seq: We extracted RNA using 3 RNAeasy columns per 50-million cell replicate and isolated polyA+ mRNA using the Poly(A)Purist MAG kit from Thermo Fisher Scientific.  PRO-Seq: We performed PRO-Seq essentially as described in Kwak H et al. Science 2013. We performed reverse transcription using SuperScript IV, then performed a junction PCR using intron-spanning primers, then finally a sequence-ready PCR.