Mondrian sp system

Sequencing libraries were prepared from 1.0 ng of DNA subjected to ChIP and input samples by a Mondrian SP+ system (Nugen) with an Ovation SP ultralow DR multiplex system (Nugen). The libraries were further purified and size-selected using an AMPure XP kit (Beckman Coulter) and were quantified by a quantitative MiSeq (qMiSeq) method (65 (link)). The samples were sequenced on a HiSeq 2500 (Illumina) that generated 101-base reads. Sequencing data were aligned with the hg19 reference genome with Bowtie2 (66 (link)), and peaks were called with MACS2 (67 (link)). ChIP-seq peak visualization was done with Integrative Genomic Viewer (68 (link)).

For the evaluation of performing exome sequencing on minute amounts of sample, sequencing library preparation was done from 1 and 10 ng DNA derived from prostate cancer tissue using Mondrian SP+ System (NuGEN Technologies Inc., CA, USA) or ThruPLEX-FD Prep Kit (Rubicon Genomics, MI, USA) according to the manufacture's recommendations. Exome capture was performed as described previously [15] (link). Custom blocking adapters were used for respective technology. For primary tumor material, whole blood of plasma, libraries were prepared ThruPLEX-FD Prep Kit (Rubicon Genomics). Exome capture was carried out using the SeqCap EZ Exome Library Version 1 (Roche Nimblegen Inc, Madison, WI, USA) according to the manufacturers instructions.