Cells were grown according to the approved ENCODE cell culture protocols. Briefly, cross-linked chromatin was immunoprecipitated with antibody, the protein:DNA crosslinks were reversed and the DNA fragments were recovered and sequenced. Because these experiments were carried out over the course of two years, several changes and improvements were made to the original protocol (see Johnson DS, et al. 2007). The major differences between -protocols are the number of cells and magnetic beads used for IP, the the +protocols are the number of cells and magnetic beads used for IP, the method of sonication used to fragment DNA, and the number of cycles of PCR used to amplify the sequencing library. The most current protocol used by the Myers Lab can be found here. The sequencing libraries labeled as PCR2x were made with two rounds of amplification (25 and 15 cycles) and those labeled as PCR1x were made with one 15-cycle round of amplification. Biological replicates from each experiment were completed. For specific details on the protocol used for a ChIP of interest (number of cells, DNA fragmentation and sequencing library construction), please contact the Myers Lab at the contact information provided below.
Libraries were sequenced with an Illumina Genome Analyzer I or an Illumina Genome Analyzer IIx according to the manufacturer's recommendations. Sequence