Sigma wga kit

The NEB Next FFPE Repair kit (NEB M6630, New England® Biolabs Inc) was used for repairing 150 ng of total DNA, according to the manufacturer’s protocol with a minor change of eluting DNA in 30 μL instead of 40 μL. A total of 10 μL of eluted DNA (total 50 ng of repaired DNA) was used for WGA using the Sigma WGA kit as described above. The remaining 100 ng of repaired DNA was used for the library prep directly using the KAPA Hyper Prep Kit.

ChIP-chip experiments were performed exactly as described in Sridharan et al. (2009) (link). Data for H3K4me3 and H3K27me3 for the iPSC line has been previously published in Sridharan et al. (2009) (link). Antibodies used were H3K4me3 (Abcam ab8580), H3K27me3 (Millipore 07-449); H3K9ac, H3K14ac, and H3K18ac were kind gifts of Prof. Michael Grunstein at UCLA; H3K9me2 (Abcam ab1220), H3K9me3 (Abcam ab8898), H3K79me2 (Activ motif-39143). Elutes were amplified using the Sigma WGA kit and applied to Agilent mouse promoter array (G4490) according to the manufacturer's instructions. Average probe signals were initially extracted in a 500-bp window-stepwise manner as described previously (Maherali et al. 2007 (link)) and then averaged across the entire 8000-bp region and used as input for the CMINT algorithm.