Antibodies were from abcam (cat#ab23738,GR77830-1) and Millipore (cat#06-680, lot#JBC1939961) and ChIP was performed using 5e6-10e6 cells per reaction. Chromatin was fixed in room temperature for 10 minutes with serum free media containing 0,37 % formaldehyde. Cells were washed twice in PBS and scraped before treatment of cell lysis buffer with protease inhibitors on ice. Pelleted nuclei were sheared to 200-700bp using an ultrasonic sonicator (Misonix). ChIP was done with 5 micrograms of antibody.  FAIRE  analysis  was  performed  according  to  the  protocol  published  by  Giresi et al . Libraries were prepared according to Bioo Scientific's instructions accompanying the DNA Sample Kit (Part# 514101). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2000 or Illumina HiSeq 2500 following the manufacturer's protocols.
GEO Accession
GSM1164154