Figure 2. The genetic landscape of L1HS-Ta insertional polymorphisms in 12 human somatic cell lines.
(a) Principle of the ATLAS-seq procedure. The subsequent in silico steps are described in Figure 2—figure supplement 1a. (b–c), Modified IGV genome browser views (Thorvaldsdóttir et al., 2013) of two non-reference polymorphic L1 instances detected in MCF7 cells (b, full length L1, note the two adjacent 5'- and 3'-ATLAS-seq peaks; c, truncated L1). (d) L1HS-Ta insertions found in the various cells of the studied panel. See also Figure 2—figure supplement 1.
Figure 2—figure supplement 1. Fixed and polymorphic L1HS-Ta elements mapped by ATLAS-seq.
(a) A scheme summarizing the principle of ATLAS-seq sequencing data analysis. (b) Barchart showing the discovery rate of fixed L1HS-Ta elements before (empty bars) and after (plain blue bars) implementation of in silico filters, in each of the analyzed cell lines. (c) Extent of L1HS-Ta insertional polymorphisms among the 12 cell lines analyzed by ATLAS-seq. (d) Venn-Diagram representing the number of common L1HS-Ta insertions, and the extent of L1-mediated structural variation, in three normal diploid cell lines (fibroblasts).