Post-conversion targeted capture of modified cytosines in Homo sapiens:IMR90
Samples were prepared by fragmenting 1 µg of input genomic DNA and 5.8 µL of bisulphite-conversion control (165 pg) in a total volume of 50 µL using a Covaris E210 series shearing instrument to an average size range of 180-220 bp.  Libraries were constructed using the KAPA HTP Library Preparation Kit Illumina (Roche NimbleGen), SeqCap Adapter Kit A and B (Roche NimbleGen), and SeqCap EZ Pure Capture Bead Kit (Roche NimbleGen).  Bisulphite conversion was done by adding 130 µL of Lightening Conversion Reagent (EZ DNA Methylation-Lightning Kit, Zymo Research) were added to the 20 µL of the DNA Sample Library. Pre-capture LM-PCR, hydrization, binding to streptavidin beads, washing, and post-capture LM-PCR of captured samples were conducted as detailed in the Roche NimbleGen SeqCap EPI user guide (http://www.nimblegen.com/products/lit/seqcap/epi/index.html). Replicates for each samples were separate library preparations from the same input genomic DNA.
IMR90-rep2-AM