Fig. 3: Systematic evaluation of known MEIs captured by nanopore Cas9 enrichment approach in different flow cells.
From: Cas9 targeted enrichment of mobile elements using nanopore sequencing
a Known L1Hs in GM12878 recovered by Cas9 targeted enrichment from the individual MinION flow cell (FAL11389), pooled-MEI MinION flow cell (FAO84736), and individual Flongle flow cell (ABB607), displayed as a proportion of the upper-bound known reference L1Hs, L1Pa, and other L1 as well as non-reference (non-ref.) L1Hs from the PacBio-MEI set. Non-reference L1Hs were divided into different subfamilies (L1Ta, L1PreTa, and L1Hs with ambiguous subfamilies). Dotted-gray line represents the intermediate values (as proportion) of MEIs that the guide RNA binds when allowing a ≤ 3 bp mismatch or gap. b Number of supporting reads of each captured L1 in the context of a. c Known AluY elements in GM12878 recovered by Cas9 enrichment on one pooled MinION flow cell (FAO84736), one individual AluYb Flongle flow cell (ACK645), and one individual AluYa Flongle flow cell (ACK655). d The number of supporting reads of each captured Alu element in the context of c. e Known SVA elements in GM12878 recovered by Cas9 enrichment on one pooled MinION flow cell (FAO84736), one individual SVA_F Flongle flow cell (ACK629), and one individual SVA_E Flongle flow cell (ACK395). f The number of supporting reads of each captured SVA element in the context of e. g Known L1Hs captured in the GM12878 trio by Cas9 enrichment on one pooled MinION flow cell (FAL15177). h The number of supporting reads of each captured non-reference L1Hs based on transmission in the GM12878 trio. The non-reference L1Hs in the parents (GM12892 and GM12891) were categorized into transmitted and not-transmitted. The non-reference L1Hs in the child (GM12878) were categorized as insertions inherited from GM12892 or GM12891, and from either parents (unknown parental lineage). In b, d, f, h, the numbers of captured MEI subfamily can be found in Supplementary Data 6 with information of mean and standard deviation; The error bars of boxplot range from Q1 − 1.5 IQR to Q3 + 1.5 IQR (IQR, interquartile range) and outliers are not shown.
