Illumina HiSeq 2500 sequencing; Leveraging cell type-specific regulatory regions to detect SNPs associated with tissue factor pathway inhibitor plasma levels
Leveraging cell type-specific regulatory regions to detect SNPs associated with tissue factor pathway inhibitor plasma levels
Chromatin immunoprecipitation experiments were conducted as previously described in (Schmidt et al. 2009). Antibodies used for ChIP were mouse anti-H3K27ac (Millipore, 05-1334 monoclonal) and rabbit anti-Jun (Santa Cruz Biotechnology, sc1694 polyclonal). EC were grown in supplier-recommended Endothelial Cell Growth Media (Cell Applications, catalogue #211-500) and cultured at 37° C in a 5%-CO2 humidified incubator. ChIP DNA was prepared for Illumina sequencing by blunt-end repair, dA-tailing, and ligation of Illumina adaptors using a NEBNext DNA library preparation kit (New England Biolabs, catalogue #E6040L). Total ChIP DNA (approximately 200-500ng) and 220ng of DNA input (WCE) was end repaired for 30 minutes at room temperature, and then purified using column purification with either DNA Clean and Concentrator (Zymogen, catalogue #D4014) or PCR purification columns (Qiagen, catalogue #28106) as recommended by manufacturer’s protocol. Blunt-end repaired DNA was dA-tailed for 40 minutes at 37° C, then column purified. dA-tailed DNA was ligated to Illumina adaptors (final concentration 6.67 nM) that have a T- overhang. USER enzyme was used to cleave the uracil hairpin of the Illumina adaptor, and adaptor-ligated DNA was column purified. The library was PCR amplified for 16-18 cycles using a universal primer and a barcoded primer (New England Biolabs, catalogue #E7335L). PCR-amplified DNA was purified using PCR column purification and eluted in 20 uL of elution buffer for preparation of gel extraction, or 30 uL of TE for preparation of Pippin Prep size selection. Library samples were size selected from 200-350bp using a 2% agarose dye-free automated size selection cassette from Pippin Prep (Sage Sciences, catalogue #CDF2010).