Chromatin was extracted using protocol described in Cain et al. 2011, except that for some samples chromatin was sheared with a Covaris S2 (settings: 40 min duty cycle 20%, intensity 8, 200 cycles/burst, 500 uL at a time in 12 x 24 mm tubes). Prepared Illumina sequencing libraries as described by the ENCODE Project Consortium (2011), starting with 20 uL of ChIP output or 4 ng of pooled input sample.
GEO Accession
GSM1164207