Comment[ArrayExpressAccession] E-GEOD-19804 Public Release Date 2011-01-30 Investigation Title Transcription profiling of lung cancer tumors from a female, non-smoking taiwanese population: Genome-wide screening of transcriptional modulation in non-smoking female lung cancer in Taiwan Comment[Submitted Name] Genome-wide screening of transcriptional modulation in non-smoking female lung cancer in Taiwan Experiment Description Although smoking is the major risk factor for lung cancer, only 7% of female lung cancer patients in Taiwan have a history of cigarette smoking, extremely lower than those in Caucasian females. This report is a comprehensive analysis of the molecular signature of non-smoking female lung cancer in Taiwan. RNA was extracted from paired tumor and normal tissues for gene expression analysis. Date of Experiment Term Source Name EFO Term Source Version Term Source File http://bar.ebi.ac.uk:8080/trac/browser/branches/curator/ExperimentalFactorOntology/ExFactorInOWL/currentrelease/eforelease/efo.owl Person Last Name Lu Lu Lai Chuang Person First Name Tzu-Pin Tzu-Pin Liang-Chuan Eric Person Mid Initials Y Person Email d96945018@ntu.edu.tw Person Affiliation National Taiwan University, Taiwan Person Phone Person Fax Person Address Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taiwan, No. 1, Sec. 4, Roosevelt Road, Taipei, Taiwan Person Roles submitter Person Roles Term Source REF Person Roles Term Accession Number Normalization Type Normalization Term Accession Number Normalization Term Source REF Replicate Type Replicate Term Accession Number Replicate Term Source REF Experimental Design Experimental Design Term Accession Number Experimental Design Term Source REF Quality Control Type Quality Control Term Accession Number Quality Control Term Source REF Protocol Name P-GSE19804-1 P-GSE19804-5 P-GSE19804-4 P-GSE19804-2 P-GSE19804-3 P-GSE19804-6 Protocol Description ID_REF =
VALUE = Log2 RMA signal intensity Chips were scanned using the GeneChip Scanner 3000 The biotinylated cRNA targets were then cleaned up, fragmented, and hybridized to GeneChip® Human Genome U133 Plus 2.0 expression arrays (Affymetrix, Inc., Santa Clara, CA). After 16 hours of hybridization at 45 °C, the arrays were washed by Fluidics Station 450 Total RNA from the tissue specimens were isolated using TRIzol® reagent (Invitrogen, Calsbad, CA) and purified with RNeasy® mini kits (Qiagen) according to the manufacturer's instructions. The IVT reaction was carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling. Background-adjusted signals were normalized by three steps: Robust Multichip Analysis (RMA), median polish method, and quantile normalization algorithm. Protocol Software Protocol Hardware Protocol Contact Protocol Type bioassay_data_transformation image_aquisition hybridization nucleic_acid_extraction labeling feature_extraction Protocol Term Source REF Protocol Term Accession Number Experimental Factor Name clinical information Experimental Factor Type clinical information Experimental Factor Term Source REF Experimental Factor Term Accession Number Publication Title Identification of a novel biomarker, SEMA5A, for non-small cell lung carcinoma in nonsmoking women. Publication Author List Lu TP, Tsai MH, Lee JM, Hsu CP, Chen PC, Lin CW, Shih JY, Yang PC, Hsiao CK, Lai LC, Chuang EY PubMed ID 20802022 Publication DOI 10.1158/1055-9965.EPI-10-0332 Publication Status published Publication Status Term Source REF EFO Publication Status Term Accession Number EFO_0001796 Comment[SecondaryAccession] GSE19804 Comment[GEOLastUpdateDate] 2011-01-30 Comment[AEExperimentType] transcription profiling by array Comment[AEExperimentDisplayName] Transcription profiling by array of human non-small cell lung cancer tissue from female non-smokers Comment[GEOReleaseDate] 2011-01-30 Comment[ArrayExpressSubmissionDate] 2010-01-08 SDRF File E-GEOD-19804.sdrf.txt