title: Sir4 ChIP sample 738
design: All chromatin immunoprecipitations (Sir4-Myc) were performed using 1% formaldehyde cross-linking of log phase cultures for 1 hour at room temperature.  IPs were performed overnight at 4 degrees C using Anti-c-Myc-Agarose (Sigma, Cat. No. A7470).  ChIP-sequencing libraries were prepared from chromatin input and Sir4 precipitate fractions as per the Illumina paired-end and ChIP-Seq protocols, with the following modifications.  Specifically, for both input and IP chromatin fractions, 1 microgram of DNA was used for library construction; melting of gel slices for size selection was performed at room temperature to prevent loss of AT-rich sequences; and 18 cycles of PCR were performed to enrich adapter-ligated fragments.  Library size and quality were verified by Bioanalyzer and quantitative PCR analysis.  Insert size, excluding adapter sequences, averaged 320 bp for all libraries.  Each input or IP library was loaded onto a single lane on a flow cell, and was sequenced by 36 bp or 45 bp paired-end reads on the Illumina Genome Analyzer II.