ChIP-seq of Primary Human Tumors

ChIP-seq for three primary human tumors was done as described previously11 (link). Chromatin was prepared from 20 to 50 sections (25 µm each) of snap-frozen tumors obtained by microtome sectioning. The following antibodies were used: H3K4me3 (1 µg/ChIP; Diagenode, C15410003-50), H3K27me3 (1 µg/ChIP; Diagenode, C15410195), H3K4me1 (1 µg/ChIP; Diagenode, C15410194), H3K27ac (1 µg/ChIP; Diagenode, C15410196), H3K56ac (4 µl/ChIP; Active Motif, 39281), H3K9me3 (1 µg/ChIP; Diagenode, C15410193), and H3K36me3 (1 µg/ChIP; Diagenode, C15410192). Library preparation for ChIP DNA and input control DNA was performed using the NEBNext Ultra kit (New England Biolabs, E7370S/L) following the manufacturer’s instructions. Quality control for the final libraries was done by measuring the DNA concentration with the Qubit dsDNA HS assay (Life Technologies, Q32851) on Qubit 2.0 Fluorometer (Life Technologies, Q32866) and by determining library fragment sizes with the Experion DNA 1K Analysis kit (Bio-Rad, 700-7107) on the Experion Automated Electrophoresis Station (Bio-Rad, 701-7000). Libraries were sequenced on Illumina HiSeq 2000/2500 machines.