Genome-Wide Analysis of IRF8 binding sites (CBX107). unidentified

For ChIP-chip analysis, chromatin-immunoprecipitated DNA samples from THP-1 cells (PMA-0h) were prepared using the antibody against IRF8 (sc6058X, Santa-cruz) with two biological replicates (1st and 2nd). The Affymetrix Human Promoter 1.0R Arrays, 25-mer probe sequences corresponding to over 25,500 human promoter regions spaced at 35 bp on the genome (NCBI version 34, hg16), were hybridized with samples in three replicates for each time points and biological replicates. Raw array data were quantile normalized within ChIP treated/control replicate groups and scaled to a median feature intensity of 500. A shift of the intensities in treatment relative to control data in a 400 bp window centered at each probe was evaluated by a Wilcoxon rank sum test, which assigned a p-value to the probe. We used the Affymetrix software, TAS for the p-value calculation. These data was converted into hg18.