title: NextSeq 500 paired end sequencing; Genome-wide identification and DNA methylation of human full-length LINE-1 (L1) retrotransposons in a panel of normal and cancer cell lines.
design: Genome-wide identification and DNA methylation of human full-length LINE-1 (L1) retrotransposons in a panel of normal and cancer cell lines.
library_construction_protocol: Cells were grown and collected from culture dishes. Growth conditions for the different cell lines is described in Philippe et al. eLife, 2016 (PMID 27016617), supplemental file 1 (https://doi.org/10.7554/eLife.13926.016) untreated Genomic DNA was extracted and prepared using QiaAmp DNA Blood mini kit (Qiagen) In brief, bs-ATLAS-seq follows these steps: fragmentation of genomic DNA by sonication, ligation of a methylated adapter, bisulfite treatment of linker-ligated DNA, suppression PCR-amplification of L1 5' junctions, and asymmetric Illumina paired-end sequencing (90 bp + 210 bp). Read #1 starts from a random position (sonicated DNA break), while read #2 starts from a fixed sequence in L1 5' UTR (internal promoter). With this design, read #2 covers the 15 most 5â€™ CpG sites (1-207, relative to L1HS consensus sequence). Read #1 has the same orientation as the L1 element.