NimbleGen (080212 RN34 CpG island Pro, Madison, WI) promoter plus CpG island tiling array has a total density of 385,000 probes that represent 19,530 rat promoters and CpG islands per slide. In this array platform, each probe contains ~50 oligonucleotides with ~50 bp gaps within the promoter and CpG island regions. These promoters and CpG islands largely overlap with transcription starting sites of RefSeq genes, covering, by average, 1.3-kb upstream and 0.5-kb downstream of the transcription starting site of 21632 transcripts. In order to avoid the biases due to false assigned promoters in intergenic regions, our analysis mainly focused on these well-annotated promoters.
