Extended Data Fig. 2: Distribution of Retain-seq reads across the genome and experimental replicates.

(a) Log-transformed mean normalized read counts of genomic bins ranked by percentile. Inset is a zoom-in of higher-percentile genomic bins showing that transfection, represented by the day 2 episome library, results in minimal dropout that does not substantially skew the sequence representation compared to the input episomal library. (b) Loss of genome-wide representation in episomal insert sequences relative to the input library over time in four cell lines assayed with Retain-seq. (c) Correlations between experimental replicates of Retain-seq across time points from different cell lines. (d) Correlation (Pearson’s R; error bands represent 95% confidence intervals) between the numbers of episomally retained elements and the sizes of their chromosomes of origin in experiments performed in various cell lines. (e) Correlation (Pearson’s R; error bands represent 95% confidence intervals) between the numbers of episomally retained elements and the sizes of their chromosomes of origin across all cell lines. (f) Distribution of genomic bin sizes containing retention elements (median 1 kb; s.d. 0.604 kb). (g) Retention of plasmids containing random genomic inserts, the EBV tethering sequence alone, or the entire EBV origin (containing both tethering and replicative sequences) compared to pUC19 in GM12878 cells (three biological replicates). Fold changes were computed using plasmid levels at day 14 post-transfection, normalizing to levels at day 2 to adjust for differential transfection efficiency across conditions. P-values computed by one-sided t-test.