GSM2197810: 519_1.5h_Pol2_Rep1; Mus musculus; ChIP-Seq
All samples, including input, were processed for library construction for Illumina sequencing  using Illumina’s TruSeq ChIP Sample Preparation Kit (Illumina cat# IP-202-  1012). In brief, DNA fragments were repaired to generate blunt ends, purified using  Agencourt AMPure XP Beads (Beckman Coulter cat# A63881), and a single “A” nucleotide  was added to each end. Double-stranded Illumina adaptors were ligated to  the fragments. Ligation products were purified using Agencourt AMPure XP Beads,  and subject to size selection using SPRIselect Beads (Beckman Coulter cat# B23318)in which both a left side size selection was performed at 0.9x volume, and a right  side size selection was performed at 0.6x volume according to manufacturer’s specifications.  Library fragments were then amplified for 16 cycles of PCR and products  were purified using Agencourt AMPure XP Beads. Constructed libraries were run on  the Agilent Bioananlyzer 2100 (Agilent Technologies) using either the DNA 7500 kit  (cat# 5067-1504) or the High Sensitivity DNA kit (cat# 5067-4626) as appropriate to  determine the average size and confirm the absence of unligated adaptors. The mean  library size is approximately 330 bp.  The ChIP-seq libraries were quantitated by qPCR using the Kapa SYBR FAST  Universal kit (Kapa Biosystems) according to the Illumina’s Sequencing Library qPCR  Quantification Guide. Libraries were multiplexed and sequenced on the Illumina HiSeq  2000 using Illumina’s kits and reagents as appropriate.  We sequenced 3 biological replicates for the 0min, 60min, 90min, 180min, and  360min time points; two biological replicates for 240min time point; and one replicate  for 40min time point.