Sequencing and read count analysis
Equal molar amounts PCR
gel-purified samples were pooled, denatured and diluted to 1.8pM, of
which 1.3 ml was sequenced on a NextSeq 550 using a high output 75 cycle
sequencing kit (Illumina). This yielded between 35 and 62 million reads
per sample. Sequencing reads were aligned to the Brunello library file
and counted using MAGeCK (Chen et al., 2018; Li et al., 2014). The raw
read counts table are in NCBI GEO (accession number GSE206996 ).