{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Kazushi Matsumura"],"study_type":["transcription profiling by array"],"organism":["Homo sapiens"],"species":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-7992"],"description":["Chronic obstructive pulmonary disease (COPD) is combination of progressive lung diseases. The diagnosis of COPD is generally based on the pulmonary function testing, however, difficulties underlie in prognosis of potential or early stage of COPD patients due to the complexity and heterogeneity of the pathogenesis. Transcriptomic technology is expected as one of the solution to resolve such complexities; therefore, we obtained transcriptomic data by in vitro testing with exposures of human 3D cultured bronchial epithelial tissues (MucilAir) to known inducible factors for early events of COPD to identify the potential descriptive marker genes. Fifteen potential biomarker genes were identified by transcriptomic analysis, and 10 out of 15 genes, as well as their coding proteins, have not been previously reported as biomarkers for chronic inflammatory lung diseases. The expression levels of these 15 genes with machine learning classification well distinguished between COPD and non-COPD patients with remarkable accuracy, suggesting these identified genes are potential descriptive marker genes for COPD."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Scaning - Command Console Software (Affymetrix) was used to automatically grid the DAT files and create the CEL files (probe cell intensity data).","Nucleic Acid Extraction - Total RNA was isolated and purified using the Qiagen RNeasy® Mini Kit (Qiagen, Hilden, Germany).","Labeling - Biotinylated cRNA was generated using GeneChip® 3′IVT PLUS Reagent Kit.","Sample Collection - MucilAir™ human bronchial epithelial cultures derived from non-smokers were purchased from Epithelix Sarl (Geneva, Switzerland). The tissues were cultured for more than 10 days for acclimation before starting exposure. The ISO Intense smoking regimen (ISO 20778: a 55-mL bell-shaped puff taken over 2 s, repeated every 30 s with blocking of filter ventilation) was used for smoking 3R4F cigarettes. The AqE was prepared by bubbling the mainstream aerosol generated from 3R4F cigarettes through PneumaCult-ALI without the supplements (StemmCell Technologies, Vancouver, BC, USA). Two 3R4F cigarettes were smoked in one smoking cycle to a butt length of 35 mm with RM20H (Borgwaldt, Hamburg, Germany), and approximately 2.0 cigarettes of 3R4F smoke were bubbled into 15 mL of ice-cold PneumaCult-ALI without supplements. The supplement of PneumaCult-ALI medium was added immediately before mixing MucilAir™ culture medium. The AqE was diluted with MucilAir™ culture medium to concentration of 0.5, 1.0, and 2.0 cigarettes/L. MucilAir™ tissue was exposed to each test substance for 4 h at the following concentrations: 8 and 16 uM (cisplatin), 50 and 100 ug/mL (bleomycin), 0.7 and 1.4 mM (NaClO), 20 and 40 uM (tBHQ), 20 and 40 ng/mL (TNF-alpha), and 20 and 40 ng/mL (IL-1beta). MucilAir™ tissue was exposed to the AqE of 3R4F smoke for 4 and 24 h at 0.5, 1.0, and 2.0 cigarettes/L. Non-treated MucilAir™ tissue was used as a control.","Hybridization - he biotin-labeled RNA was Hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array using GeneChip® Hybridization, Wash and Stain Kit."],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","MAGE-TAB Files","Array Designs"],"pubmed_authors":["Kazushi Matsumura"],"additional_accession":[]},"is_claimable":false,"name":"Transcription profiling by array of three-dimensional human bronchial epithelial cultures (MucilAir) treated with cigarette smoke, sodium hypochlorite (NaClO), tert-butyl hydroquinone (tBHQ), cisplatin, bleomycin, TNF-alpha, and IL-1beta.","description":"Chronic obstructive pulmonary disease (COPD) is combination of progressive lung diseases. The diagnosis of COPD is generally based on the pulmonary function testing, however, difficulties underlie in prognosis of potential or early stage of COPD patients due to the complexity and heterogeneity of the pathogenesis. Transcriptomic technology is expected as one of the solution to resolve such complexities; therefore, we obtained transcriptomic data by in vitro testing with exposures of human 3D cultured bronchial epithelial tissues (MucilAir) to known inducible factors for early events of COPD to identify the potential descriptive marker genes. Fifteen potential biomarker genes were identified by transcriptomic analysis, and 10 out of 15 genes, as well as their coding proteins, have not been previously reported as biomarkers for chronic inflammatory lung diseases. The expression levels of these 15 genes with machine learning classification well distinguished between COPD and non-COPD patients with remarkable accuracy, suggesting these identified genes are potential descriptive marker genes for COPD.","dates":{"release":"2020-01-22T00:00:00Z","modification":"2022-02-02T14:52:46.658Z","creation":"2022-02-02T14:52:46.658Z"},"accession":"E-MTAB-7992","cross_references":{"EFO":["EFO_0002768","EFO_0003814","EFO_0002944","EFO_0003813","EFO_0005518","EFO_0003815"]}}