title: troph_rep1_input
design: ChIP and input DNA libraries were prepared using the NEBNext ultra DNA library prep kit for Illumina (New England BioLabs, E7370) from 6 ng input or chromatin immunoprecipitated DNA without size selection. The PCR amplification step was performed using 1 unit of high fidelity KAPA HiFi DNA polymerase (KAPA biosystems, KK2101), 0.3 mM dNTPs, 0.5 M NEBNext Universal PCR Primers for Illumina and 0.5 M NEBNext Index Primer for Illumina (NEBNext Multiplex Oligos for Illumina Index Primers Set 1 (E7335) and Set 2 (E7500)) in 1 x KAPA HiFi buffer containing tetramethylammonium chloride for 12 PCR cycles. The PCR conditions were 98C for 2 minutes for the initial denaturation followed by 12 cycles of 98C for 15 seconds and 65C for 2 minutes and a final extension at 65C for 5 minutes. Library clean-up was performed using 1 x AMPure beads and DNA libraries were eluted with 10 mM Tris-HCl pH 7.5. The libraries were sequenced on a HiSeq2500 (Illumina) generating126 bp paired-end reads.