| Construction Protocol | Input for ChIP analyses were performed as described in Pasini et al. (2008). MNase digested DNA prepared for sequencing with the Illumina ChIPSeq Sample Prep kit. DNA libraries were quantified using a bioanalyzer (Agilent) and diluted to 5-10 pM. Diluted libraries were used directly for cluster generation and sequencing analysis using the Genome Analyzer IIx (Illumina) following the protocol of the manufacturer. Basecalling and mapping of the 36 bp sequences were done using illumina RTA SCS2.6 allowing up to two mismatches in the first 35 bases of a read against mouse genomes July 2007 release (mm9). |
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