biostudies-arrayexpressEllen JorgensenHomo sapiensMicroArraySuite 5.0https://www.ebi.ac.uk/biostudies/studies/E-GEOD-10700Gene expression patterns were assessed in normal human bronchial epithelial (NHBE) cells exposed to cigarette smoke from a reference cigarette (2R4F, University of Kentucky) and a typical American brand of "light" cigarettes ("Lights") in order to develop a better understanding of the genomic impact of tobacco exposure, which can ultimately define biomarkers that discriminate tobacco-related effects and outcomes in a clinical setting. NHBE cells were treated with whole cigarette smoke for 15 minutes and alterations to the transcriptome assessed at 2, 4, 8 and 24 hours post-exposure using high-density oligonucleotide microarrays. Experiment Overall Design: 4 replicate Petri dishes of cells were exposed in a custom-built smoke exposure chamber. Cigarettes were smoked as per FTC protocols, and the smoke diluted such that the cells were at least 50% viable as compared to mock (air)-exposed controls after 24h. RNA from each replicate dish was analyzed using a separate array. Four replicates of an incubator (untreated with either smoke or air) are included also.biostudies-arrayexpressGrowth Protocol - NHBE cells were cultured in complete Bronchial Epithelial Cell Growth Medium, prepared by supplementing Bronchial Epithelial Basal Medium with retinoic acid, epidermal growth factor, epinephrine, transferrin, T3, insulin, hydrocortisone, antimicrobial agents and bovine pituitary extract by addition of SingleQuots,TM (Cambrex Corporation).Labeling - Two micrograms of total RNA was reverse transcribed into double stranded cDNA using a oligo(dT)/T7 promotor chimeric primer, and in vitro transcribed using reagents provided by Affymetrix (Santa Clara, CA).Sample Processing - In a custom-built smoke exposure chamber, NHBE cells were exposed to 15min FTC smoking with each 35mL puff diluted into 500cc air. Following exposure the medium was replaced with fresh and the cells placed in a 37C incubator for the times indicated.Hybridization - Fragmented biotin-labeled cRNA at a concentration of 50 ng/ul was hybridized to Affymetrix Human Genome U133 Plus 2.0 GeneChip® expression arrays according to the manufacturer’s recommendations for a minimum of sixteen hours. Post-hybridization washing and staining was performed on the GeneChip® Fluidics Station 450Nucleic Acid Extraction - total RNA was extracted using Qiagen Rneasy kits according to manufacturer's instructionsMIAME ScoreRaw DataOrganizationAssays and DataProcessed DataAdditional FilesMAGE-TAB FilesArray DesignsAssay Data Transformation - Title: Affymetrix CHP Analysis (ExpressionStat). Description:Feature Extraction - Title: Affymetrix CEL analysis. Description:UnknownTranscriptomicsGenomicsProteomicstranscription profiling by arrayHomo sapiensEllen JorgensenfalseTranscription profiling of human NHBE cells exposed TO NORMAL human bronchial epithelial whole cigarette smoke FROM light AND standard brandsGene expression patterns were assessed in normal human bronchial epithelial (NHBE) cells exposed to cigarette smoke from a reference cigarette (2R4F, University of Kentucky) and a typical American brand of "light" cigarettes ("Lights") in order to develop a better understanding of the genomic impact of tobacco exposure, which can ultimately define biomarkers that discriminate tobacco-related effects and outcomes in a clinical setting. NHBE cells were treated with whole cigarette smoke for 15 minutes and alterations to the transcriptome assessed at 2, 4, 8 and 24 hours post-exposure using high-density oligonucleotide microarrays. Experiment Overall Design: 4 replicate Petri dishes of cells were exposed in a custom-built smoke exposure chamber. Cigarettes were smoked as per FTC protocols, and the smoke diluted such that the cells were at least 50% viable as compared to mock (air)-exposed controls after 24h. RNA from each replicate dish was analyzed using a separate array. Four replicates of an incubator (untreated with either smoke or air) are included also.2008-04-06T00:00:00Z2022-11-26T23:46:02.781Z2022-02-02T21:30:06.013ZE-GEOD-10700GSE10700EFO_0002768