title: Sequence capture Bisulfite-Seq Zea mays B4-2_A188_B4_R1
design: SeqCap libraries were constructed as described previously (Li et al. 2015a). Briefly, DNA of maize-embryo-derived callus, regenerated plants, and non-cultured control plants were isolated using the standard CTAB method. Five hundred to 1,000 nanograms of genomic DNA was used for sequence capture library construction. DNA was sheared to fragments between 180 and 250 bp. The fragments were subject to end repair, dA tailing, ligating to index adapters, and Dual-SPRI Size Selection, followed by bisulfite conversion. The bisulfite converted libraries were then subject to Pre-Capture LM-PCR amplification, purification and quantified using a PicoGreen dsDNA Assay Kit. Then the amplified sample library was hybridized to probes designed to target the set of genomic regions selected for analysis. After hybridization, the captured DNA library was bounded to capture beads and the bead-bound DNA was washed. Post-Capture LM-PCR amplification was performed, and following PCR cleanup the libraries were quantitated using PicoGreen. Libraries were pooled together in several batches and the pools sequenced over multiple lanes at the University of Minnesota Genomics Center on a HiSeq2500, in High-output 2x125 bp paired end (PE) mode.