Extended Data Fig. 1: Optimization of Retain-seq library preparation.

(a) Insert size distribution of genomic fragments included in the input mixed episome library. (b) Genome-wide coverage of sequenced reads derived from input episome library. (c) Left: Representative quantitative PCR amplification curves across varying amounts of episome library as PCR input. Right: Log-transformed mean normalized read counts of genomic bins ranked by percentile. Inset is a zoom-in of the higher-percentile genomic bins, in which a 100-fold range of DNA amounts from 0.1 ng – 10 ng of input showed highly comparable representation (despite some library dropout at 0.1 ng of input DNA) while 0.01 ng PCR input showed substantial library dropout and signs of skewing and was used to set the quality threshold for all library preparations. See Methods. (d) Log-transformed mean normalized read counts of genomic bins ranked by percentile. Inset is a zoom-in of the higher-percentile genomic bins showing that increasing PCR cycles during library preparation alters skewing of sequencing reads.