Cells were harvested and DNA was extracted using the NucleoSpin Tissue kit (Macherey-Nagel GmbH & Co. KG, Düren, Germany). Libraries for whole-genome sequencing were prepared with the NEBNext Ultra II FS DNA Library Prep Kit for Illumina (New England BioLabs, Inc., Ipswich, MA). Libraries were sequenced on a MGISEQ-2000 (NGP; MGI Tech Co. Ltd, Shenzhen, China), HiSeq X (IMR-5/75, Kelly; Illumina, Inc., San Diego, CA), and NovaSeq 6000 (CHP-212; Illumina, Inc., San Diego, CA) with 2 × 150 bp paired-end reads. Quality control, adapter trimming, alignment, duplicate removal as for ChIP-seq data. Copy-number variation was called (Control-FREEC58 (link) 11.4 with default parameters). Structural variants were called using SvABA59 (link) (1.1.1) in germline mode and discarding regions in a blacklist provided by SvABA (https://data.broadinstitute.org/snowman/svaba_exclusions.bed).
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