ChIP-chip analysis of c-Myc and E2F4 was performed using 2091 foreskin fibroblasts and HeLa cells. ChIP was carried out from normally-growing HeLa cells and from 2091 quiescent (0.1% serum FBS), as well as serum-stimulated (10% FBS, 4hrs), fibroblasts. Microarray hybridizations were performed using NimbleGen ENCODE arrays and protocols.
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Chromatin from each cell line under a given condition was cross-linked with 1% formaldehyde, sheared, precipitated with antibody, and reverse cross-linked to obtain enriched DNA fragments. ChIP material was amplified and hybridized to a NimbleGen ENCODE region array. The raw and processed files reflect fold enrichment over the mock ChIP sample, which was used as a reference in the hybridization.
Each of the four experiments has three independent biological replicates. Data from all three replicates were averaged to generate a single data file. The NimbleGen method for hit identification was used to generate the peaks at a false positive rate of <= 0.05.
These data were contributed by Jonghwan Kim, Akshay Bhinge, and Vishy Iyer from the Iyer lab at the University of Texas at Austin, in collaboration with Mike Singer, Nan Jiang, and Roland Green of NimbleGen Systems, Inc.
Kim, J., Bhinge, A., Morgan, X.C. and Iyer, V.R. Mapping DNA-protein interactions in large genomes by sequence tag analysis of genomic enrichment. Nature Methods 2, 47-53 (2005).