Transcriptomics,Genomics

Dataset Information

17

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


ABSTRACT: 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 Overall design: 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.

INSTRUMENT(S): [Hs35b_M01R] Affymetrix Human Tiling 1.0R Set, Array 1

SUBMITTER: Damon Scott Perez   

PROVIDER: GSE9655 | GEO | 2007-11-22

SECONDARY ACCESSION(S): PRJNA103527

REPOSITORIES: GEO

altmetric image

Publications

Long, abundantly expressed non-coding transcripts are altered in cancer.

Perez Damon S DS   Hoage Tiffany R TR   Pritchett Jay R JR   Ducharme-Smith Allison L AL   Halling Meredith L ML   Ganapathiraju Sree C SC   Streng Paul S PS   Smith David I DI  

Human molecular genetics 20071115 5


Recent studies with tiling arrays have revealed more genomic transcription than previously anticipated. Whole new groups of non-coding transcripts (NCTs) have been detected. Some of these NCTs, including miRNAs, can regulate gene expression. To date, most known NCTs studied have been relatively short, but several important regulatory NCTs, including XIST, MALAT-1, BC1 and BC200, are considerably larger in length and represent a novel class of long, non-coding RNA species. Whole-genome tiling arr  ...[more]

Similar Datasets

2009-06-10 | GSE16086 | GEO
2012-03-27 | E-GEOD-16086 | ArrayExpress
| GSE49001 | GEO
2014-05-03 | E-GEOD-49001 | ArrayExpress
| GSE84002 | GEO
2007-02-06 | GSE6921 | GEO
2013-04-25 | E-GEOD-41749 | ArrayExpress
| PRJNA98141 | ENA
2014-05-03 | E-GEOD-25856 | ArrayExpress
2008-05-14 | GSE10834 | GEO