the same cells were amplified using two-step PCR with primers containing sample barcodes to separately tag cDNA (representing expression from an allele) and input DNA from each replicate, unique molecular indices (UMI), and partial Illumina sequencing adapters (Illumina, San Diego, CA). The resulting PCR products of cDNAs and plasmid DNAs from each cell type were pooled to minimize potential batch effects in library preparation and sequencing. These PCR products were amplified using barcoded Illumina index adaptors and the two resulting libraries were pooled in equal molarity (again, to minimize batch effects) and sequenced (75 base paired-ends) on the Illumina HiSeq 4000 1 lane each at 2 different times.
