ONTOLOGY SOURCE REFERENCE Term Source Name "CHEBI" "HP" "OBI" "EFO" "BTO" "NCBITAXON" "PATO" "XCO" "FMA" "MESH" "UO" "DOID" Term Source File "http://data.bioontology.org/ontologies/CHEBI" "http://data.bioontology.org/ontologies/HP" "http://data.bioontology.org/ontologies/OBI" "http://data.bioontology.org/ontologies/EFO" "http://data.bioontology.org/ontologies/BTO" "http://data.bioontology.org/ontologies/NCBITAXON" "http://data.bioontology.org/ontologies/PATO" "http://data.bioontology.org/ontologies/XCO" "http://data.bioontology.org/ontologies/FMA" "http://data.bioontology.org/ontologies/MESH" "http://data.bioontology.org/ontologies/UO" "http://data.bioontology.org/ontologies/DOID" Term Source Version "78" "408" "21" "111" "20" "2" "160" "33" "3" "5" "42" "399" Term Source Description "Chemical Entities of Biological Interest Ontology" "Human Phenotype Ontology" "Ontology for Biomedical Investigations" "Experimental Factor Ontology" "BRENDA Tissue and Enzyme Source Ontology" "National Center for Biotechnology Information (NCBI) Organismal Classification" "Phenotypic Quality Ontology" "Experimental Conditions Ontology" "Foundational Model of Anatomy" "Medical Subject Headings" "Units of Measurement Ontology" "Human Disease Ontology" INVESTIGATION Investigation Identifier "GSE11138" Investigation Title "Investigation" Investigation Description "" Investigation Submission Date "" Investigation Public Release Date "" Comment [Created with configuration] "" Comment [Last Opened With Configuration] "" Comment[Created With Configuration] "" Comment[Last Opened With Configuration] "" INVESTIGATION PUBLICATIONS Investigation PubMed ID "" Investigation Publication DOI "" Investigation Publication Author List "" Investigation Publication Title "" Investigation Publication Status "" Investigation Publication Status Term Accession Number "" Investigation Publication Status Term Source REF "" INVESTIGATION CONTACTS Investigation Person Last Name "" Investigation Person First Name "" Investigation Person Mid Initials "" Investigation Person Email "" Investigation Person Phone "" Investigation Person Fax "" Investigation Person Address "" Investigation Person Affiliation "" Investigation Person Roles "" Investigation Person Roles Term Accession Number "" Investigation Person Roles Term Source REF "" STUDY Study Identifier "GSE11138" Study Title "Left anterior descendent (LAD) coronary artery atherosclerotic plaque gene expression" Study Description "Transcriptional profiling of atherosclerotic plaques from the left anterior descendent (LAD) coronary arteries of 8 patients with ł75% stenosis. 2-channel microarray analysis; second channel = pooled RNA from 10 control LAD coronary arteries without plaque. Each slide was scanned three times at low, medium and high sensitivity, plus technical replicates. See original GEO entry and Table 1 from paper for details on control patients. Inferred comorbidities shown are inferred from drug types." Comment[Study Grant Number] "" Comment[Study Funding Agency] "" Study Submission Date "" Study Public Release Date "2009-01-16" Study File Name "s_GSE11138_study_sample.txt" STUDY DESIGN DESCRIPTORS Study Design Type "" Study Design Type Term Accession Number "" Study Design Type Term Source REF "" STUDY PUBLICATIONS Study PubMed ID "19134193" Study Publication DOI "10.1186/1471-2164-10-13" Study Publication Author List "Cagnin S, Biscuola M, Patuzzo C, Trabetti E, Pasquali A, Laveder P, Faggian G, Iafrancesco M, Mazzucco A, Pignatti PF, Lanfranchi G." Study Publication Title "Reconstruction and functional analysis of altered molecular pathways in human atherosclerotic arteries." Study Publication Status "Published" Study Publication Status Term Accession Number "" Study Publication Status Term Source REF "" STUDY FACTORS Study Factor Name "" Study Factor Type "" Study Factor Type Term Accession Number "" Study Factor Type Term Source REF "" STUDY ASSAYS Study Assay File Name "a_GSE11138_mapped_study_transcription_profiling_DNA_microarray.txt" Study Assay Measurement Type "transcription profiling" Study Assay Measurement Type Term Accession Number "http://purl.obolibrary.org/obo/OBI_0000424" Study Assay Measurement Type Term Source REF "OBI" Study Assay Technology Type "DNA microarray" Study Assay Technology Type Term Accession Number "http://purl.obolibrary.org/obo/OBI_0400148" Study Assay Technology Type Term Source REF "OBI" Study Assay Technology Platform "Micro-CRIBI Human Oligo Array V_0 (Operon V2.0)" STUDY PROTOCOLS Study Protocol Name "RNA extraction" "labeling" "nucleic acid hybridization" "data collection" "normalization data transformation" "data transformation" "patient selection" "surgical dissection" Study Protocol Type "RNA extraction" "labeling" "nucleic acid hybridization" "data collection" "normalization data transformation" "data transformation" "patient selection" "surgical dissection" Study Protocol Type Term Accession Number "" "" "" "" "" "" "" "" Study Protocol Type Term Source REF "" "" "" "" "" "" "" "" Study Protocol Description "Total RNA was extracted with TRIzol method (Invitrogen). The procedure was: 1. Homogenization of the coronary fragments, dimensionally homogeneous, by the IKA¨ Werke (GmbH & Co.) homogenizer; 2. Incubation, at room temperature, for 15 minutes; 3. Addition of 0.2ml/1ml Trizol and shake for 1 minute; 4. Leave in ice for 15 minutes and then centrifuge at 4ˇ C for 20 minutes at 14,000 X g; 5 Transfer the supernatant to 1.5 ml microfuge non-stick tubes and add an equal volume of isopropanol to precipitate the RNA; 6. Incubate at -20ˇ C for one hour and centrifuge at 4ˇ C for 20 minutes at 14,000 X g; 7. Discard the supernatant and wash with ethanol 75% three times centrifuging every time for 15 minutes at 4ˇ C at 14,000 X g; 8. Pellet was resuspended in ultraPUREŞ distilled water DNase, RNase Free (Gibco). Extracted total RNA was quantized by UV adsorption in a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific) and analyzed for quality by capillary electrophoresis in an Agilent 2100 Bioanalyzer. All RNAs utilized in this study presented RIN at least 7. Extracted total RNA was quantized by UV adsorption in a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific) and analyzed for quality by capillary electrophoresis in an Agilent 2100 Bioanalyzer. All RNAs utilized in this study presented RIN at least 7." "" "Ranges along 350 and 300 pico-moles and 2.7 and 3.0 µg of aRNA labeled with Cy3 and Cy5 were co-precipitated with the ammonium acetate and ethanol. Pellet was resuspended in 110 µl with the hybridization solution composed by SSC 5X, SDS 0.1%, Formamide 25% and salmon sperm purified DNA 100 ng/µl and carried out in an automatic hybridization station (ArrayBooster, Advalytix) at 48ˇ C for 30 hours in the competitive hybridization. Microarray slides, before hybridization, have been blocked with the pre-hybridization solution (SSC 5X, SDS 0.1%, salmon sperm purified DNA 100 ng/ul and Denhardt's solution 5X) for 8 hours at 48ˇ C. After the hybridization slides were washed at room temperature with 1X SSC 0.2% SDS for 4 minutes one time; 0.1X SSC 0.2% SDS for 4 minutes one time; 0.2X SSC for 3 minutes two times each with new solution and 0.1X SSC for 3 minutes one time. Slides were dried centrifuging 1 minute at 800 X g at 20ˇ C." "After stringent washings, fluorescence left in the microarray slides were read with the ScanArray LITE confocal laser scanner (PerkinElmer) with 5 µm resolution. Each slide was subjected to three consecutive scans at low, medium and high settings of laser and photomultiplier. This protocol allows for a wide dynamic range of detection spectrum of fluorescent spots in the microarray like proposed by Skibbe et al. (Bioinformatics. 2006;22(15):1863-1870) . Low, intermediate and high intensity scans images were quantified with ScanArray Express (PerkinElmer) software using the fixed circle method." "Data from each of three scan intensities (low, medium, high) were analyzed separately. Fluorescence intensity was determined with the ScanArray Express software (PerkinElmer) using fixed circle method and median spot intensity background subtracted was normalized in the MIDAW tool using sequentially global mean normalization and local mean normalization (LOWESS) methods. Lowess normalization was performed without distinguishing between different sub-arrays." "Normalized log2(patient_ch1/controls_ch2) values were filtered according to the median of the value calculated in the empty array position for the average of the Ch1% > BKG + 1 SD and Ch2% > BKG + 1 SD values. Ch1% or Ch2% > BKG + 1 SD value is the percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity. Processing for data filtering is here summarized: 1. calculate average for Ch1% > BKG + 1 SD and Ch2% > BKG + 1 SD for each gene; 2. calculate median of the average calculated in point 1 for the empty position (see table description for experiments filtering on supplementary data table); 3. exclude normalized gene expression values presenting average calculated in point 1 under median calculated in point 2 for each experiment; 4. generated expression matrix was loaded in to TIGR MeV software and filtered for missing values along experiments. Only genes presenting calculated value in all experiment but one were used to identify differentially expressed genes by SAM software; 5. differentially expressed genes calculated at the point 4 for each scan type (high, medium and low) were integrated." "18 patients were recruited at the Cardio-Chirurgic Section of the University Hospital Borgo Trento (Verona, Italy) for heart transplantation or by-pass surgery. According to clinical diagnosis and angiography, patients were subdivided in atherosclerotic with at least 75% stenosis and non-atherosclerotic controls. Before and during heart transplantation, cases were subjected to standard oral medication with aspirin." "LAD coronaries were dissected from diseased hearts immediately after surgical removal, cleaned from fatty and cardiac muscle tissues and starved in RNAlater Solution (Ambion) for further microscopy and gene expression analysis. 5-?m-thick serial sections of paraffin included coronaries fragments were used for hematoxylin-eosin staining and microscopic analysis. Visible plaques and LAD controls, adjacent to the segment utilized for histochemical analysis, were dissected from the entire coronary fragment and used separately for total RNA extraction with TRIzol (Invitrogen)." Study Protocol URI "" "" "" "" "" "" "" "" Study Protocol Version "" "" "" "" "" "" "" "" Study Protocol Parameters Name "" "" "" "" "" "" "" "" Study Protocol Parameters Name Term Accession Number "" "" "" "" "" "" "" "" Study Protocol Parameters Name Term Source REF "" "" "" "" "" "" "" "" Study Protocol Components Name "" "" "" "" "" "" "" "" Study Protocol Components Type "" "" "" "" "" "" "" "" Study Protocol Components Type Term Accession Number "" "" "" "" "" "" "" "" Study Protocol Components Type Term Source REF "" "" "" "" "" "" "" "" STUDY CONTACTS Study Person Last Name "" Study Person First Name "" Study Person Mid Initials "" Study Person Email "" Study Person Phone "" Study Person Fax "" Study Person Address "" Study Person Affiliation "" Study Person Roles "" Study Person Roles Term Accession Number "" Study Person Roles Term Source REF ""