ONTOLOGY SOURCE REFERENCE
Term Source Name	"ArrayExpress"	"EFO"	"NCBITaxon"	"CHEBI"	"HP"	"MSH"	"ICD10CM"	"UO"	"NCIt"	"SNOMEDCT"	"BTO"	"CSP"	"EV"	"GeXO"	"IMR"	"LSM"	"PR"	"CL"	
Term Source File	"http://www.ebi.ac.uk/arrayexpress/"	"http://www.ebi.ac.uk/efo/efo.owl"	"http://bioportal.bioontology.org/ontologies/47845"	"http://bioportal.bioontology.org/ontologies/50716"	"http://bioportal.bioontology.org/ontologies/50756"	"http://bioportal.bioontology.org/ontologies/46836"	"http://bioportal.bioontology.org/ontologies/46302"	"http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=UO"	"http://bioportal.bioontology.org/ontologies/50586"	"http://bioportal.bioontology.org/ontologies/46896"	"http://bioportal.bioontology.org/ontologies/50688"	"http://bioportal.bioontology.org/ontologies/44432"	"http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=EV"	"http://bioportal.bioontology.org/ontologies/49482"	"http://bioportal.bioontology.org/ontologies/45784"	"http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=LSM"	"http://bioportal.bioontology.org/ontologies/50525"	"http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=CL"	
Term Source Version	""	""	"47845"	"50716"	"50756"	"46836"	"46302"	"Jun 2010"	"50586"	"46896"	"50688"	"44432"	"Jun 2010"	"49482"	"45784"	"Jun 2010"	"50525"	"Jun 2010"	
Term Source Description	""	""	"National Center for Biotechnology Information (NCBI) Organismal Classification"	"Chemical Entities of Biological Interest Ontology"	"Human Phenotype Ontology"	"Medical Subject Headings"	"International Classification of Diseases, Version 10 - Clinical Modfication"	"Unit Ontology"	"National Cancer Institute Thesaurus"	"Systematized Nomenclature of Medicine - Clinical Terms"	"BRENDA Tissue and Enzyme Source Ontology"	"Computer Retrieval of Information on Scientific Projects Thesaurus"	"eVOC (Expressed Sequence Annotation for Humans)"	"Gene Expression Ontology"	"Molecule Role Ontology"	"Leukocyte Surface Markers"	"Protein Ontology"	"Cell Type"	
INVESTIGATION
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INVESTIGATION PUBLICATIONS
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STUDY
Study Identifier	"E-GEOD-9820"
Study Title	"Trancriptional profiling of five classes of white blood cells in patients with coronary artery disease. [original title: Circulating Mononuclear Cell Transcriptomes in Patients with Atherosclerotic Coronary Artery Disease]"
Study Description	"18 patients with severe triple-vessel coronary artery disease (CAD) were matched to 13 control patients who had no sign of CAD but who had been admitted with chest pain and likelihood of CAD. All patients were on aspirin and statin treatment. The following types of cells were isolated: macrophages, resting monocytes, stem cells, stimulated monocytes, and T cells. Refer to supplementary methods for the detailed separation protocol and supplementary table 1 for additional details on patient characteristics including medical history and lab scores; due to ambiguities, however, it is not possible to distinguish patient A11 from A35 or patient A7 from A37. Patients were excluded if they had a myocardial infarction within the last four weeks, acute coronary syndrome, diabetes mellitus, neoplastic disease, or systemic inflammatory disease. [original description: Monocytes and T-cells play an important role in the development of atherosclerotic coronary artery disease (CAD). Differences in transcriptional activity of these cells might reflect the individual's atherosclerotic burden. Transcriptome analysis of circulating mononuclear cells from carefully matched atherosclerotic and control patients will potentially provide insights into the pathophysiology of atherosclerosis and supply biomarkers for diagnostic purposes. From patients undergoing coronary angiography because of anginal symptoms, we carefully matched 18 patients with severe triple-vessel CAD to 13 control patients without signs of CAD on angiography. All patients were on statin and aspirin treatment. RNA from circulating CD4+ T-cells, CD14+ monocytes, lipopolysaccharide-stimulated monocytes, macrophages and CD34+ progenitor cells was subjected to genome-wide expression analysis. Only CD14+ monocytes demonstrated that a small number of genes involved in activation was overexpressed in control patients, which was verified by real-time polymerase-chain reaction. In this pilot study, cautious matching of patients with severe atherosclerotic CAD with control patients without angiographic signs of coronary atherosclerosis did not reveal differences in transcriptional activity in four out of five different mononuclear cell types. In resting monocytes from patients without overt CAD some inflammatory genes were overexpressed as compared to patients with severe CAD. Large inter-individual variability prevented the use of single differentially expressed genes as biomarkers. Keywords: disease-state analysis In total 153 arrays were analyzed with 6 technical replicates (147 biological samples). CD34+ stem cells, CD4+ T-cells, resting CD14+ monocytes, stimulated monocytes and macrophages were analyzed, all from patient with severe coronary atherosclerosis or controls that had no coronary atherosclerosis as determined angiographically, and which were carefully matched for age and gender.]"
Comment[Study Grant Number]	""
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Study Public Release Date	"2008-12-01"
Study File Name	"s_E-GEOD-9820_study_samples.txt"
STUDY DESIGN DESCRIPTORS
Study Design Type	"transcription profiling by array"
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STUDY PUBLICATIONS
Study PubMed ID	"19059264"
Study Publication DOI	"10.1016/j.yjmcc.2008.10.029"
Study Publication Author List	"Schirmer SH, Fledderus JO, van der Laan AM, van der Pouw-Kraan TC, Moerland PD, Volger OL, Baggen JM, Böhm M, Piek JJ, Horrevoets AJ, van Royen N"
Study Publication Title	"Suppression of inflammatory signaling in monocytes from patients with coronary artery disease."
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STUDY FACTORS
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STUDY ASSAYS
Study Assay File Name	"a_E-GEOD-9820_GeneChip_assay.txt"
Study Assay Measurement Type	"transcription profiling"
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Study Assay Technology Type	"DNA microarray"
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STUDY PROTOCOLS
Study Protocol Name	"P-GSE9820-2"	"P-GSE9820-3"	"P-GSE9820-4"	"P-GSE9820-5"	"P-GSE9820-6"	"P-GSE9820-1"
Study Protocol Type	"growth protocol"	"nucleic acid extraction protocol"	"labeling protocol"	"hybridization protocol"	"array scanning protocol"	"normalization data transformation protocol"
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Study Protocol Description	"Using immunomagnetic beads (Dynabeads, Invitrogen, Carlsbad, CA), CD14+ monocytes, CD4+ T-cells and CD34+ stem cells were positively isolated for direct cell lysis, while negatively isolated monocytes were split into two fractions for stimulation with 10 ng/ml lipopolysaccharide (LPS) for 3h, or for 20h cell culture towards macrophages."	"Positively isolated monocytes, T-cells and stem cells as well as cultured stimulated monocytes and macrophages were lysed and total RNA was isolated (Absolutely RNA Microprep Kit, Stratagene, La Jolla, CA)."	"Total RNA samples were amplified and biotinylated using the Illumina TotalPrep RNA amplification Kit (Ambion, Austin, TX)."	"According to beadchip array manufacturer's protocol"	"According to beadchip array manufacturer's protocol"	"Array data were extracted using Illumina's BeadStudio software. From 13 controls and 18 patients we analyzed CD14+ monocyte, CD4+ T-cell, LPS-stimulated monocytes and macrophage samples, in total 130 arrays (including 6 technical replicates). From the CD34+ cell samples, only 23 passed quality control and were analyzed by array, giving a grand total of 153 arrays. Normalization and statistical analysis of the bead summary data from the arrays was carried out using the limma package14 and in-house scripts in R/Bioconductor. Bead summary intensities were log2-transformed and then normalized using quantile normalization. To find differentially expressed genes, we performed a linear model analysis. Technical replicates were handled by estimating a common value for the intra-replicate correlation and including it in the linear model. Differential expression between the treatments of interest was assessed using a moderated t-test. This test is similar to a standard t-test for each probe except that the standard errors are moderated across genes to ensure more stable inference for each gene. Resulting p-values were corrected for multiple testing using the Benjamini-Hochberg false discovery rate. ID_REF =  VALUE = log2 normalized signal intensity"
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STUDY CONTACTS
Study Person Last Name	"Schirmer"	"Schirmer"	"Fledderus"	"Horrevoets"	"Royen"
Study Person First Name	"Stephan"	"Stephan"	"Joost"	"Anton"	"N"
Study Person Mid Initials	"Henrik"	"H"	"O"	"J"	"V"
Study Person Email	"stephan.schirmer@uks.eu"	""	""	""	""
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Study Person Address	"Cardiology, Academic Medical Center, Meibergdreef 9, Amsterdam, Netherlands"	""	""	""	""
Study Person Affiliation	"Academic Medical Center"	""	""	""	""
Study Person Roles	"submitter"	""	""	""	""
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