Whole-genome tiling array analysis in normal human bronchial/tracheal epithelial cells (NHBE)

Identify transcriptionally-active regions (TARs) greater than 400 nt long across the entire human genome. A total of 578 were identified in NHBE cells. We then focused on those TARs originating from non-coding sequence and that displayed a moderate to high degree of sequence conservation. A subset of 15 non-coding transcripts were then further examined to determine if they are altered in cancer (deregulated expression in breast and ovarian cancer and sequenced for mutations in a panel of cancer samples). Only transcriptionally-active regions originating from non-coding sequence, expressing at the 99.5th percentile, and longer than 400 nt were examined so far in our studies. Keywords: whole-genome mapping, transcriptionally-active regions, tiling arrays, non-coding transcripts, bronchial/tracheal epithelial cells Total RNA isolated from NHBE cell cultures were labeled and hybridized to 3 sets of the GeneChip® Human Tiling 1.0R Array set of 14 (3 x 14 = 49 chips total) according to supplier's protocol. A total of 3 biological replicates were run. Each biological replicate was run on an entire set of 14 chips which covers the entire non-repetitive portion of the human genome. The first 2 sets were labeled and hybridized together and the 3rd set was hybridized at a later date. Also, for the first 2 tiling array sets, ribosomal RNA removal was not part of the initial protocol. However, since we ran the 3rd set at a later date the protocol changed and included a ribosomal removal step.