ONTOLOGY SOURCE REFERENCE
Term Source Name	"mo"	"efo.obo"	"EFO"	"The MGED Ontology"	"ArrayExpress"	"NCBITaxon"	"CHEBI"	"ODGI"	"DOID"	"PATO"	"MSH"	"BTO"	"SNOMEDCT"	"CSP"	"OBI"	
Term Source File	"http://mged.sourceforge.net/ontologies/MGEDontology.php"	"/nfs/ma/ma-exp/GEOImportDownload/efo.obo"	"http://www.ebi.ac.uk/efo/"	"http://www.ebi.ac.uk/arrayexpress"	""	"http://bioportal.bioontology.org/ontologies/47845"	"http://bioportal.bioontology.org/ontologies/50526"	"http://bioportal.bioontology.org/ontologies/49709"	"http://bioportal.bioontology.org/ontologies/50310"	"http://bioportal.bioontology.org/ontologies/50280"	"http://bioportal.bioontology.org/ontologies/46836"	"http://bioportal.bioontology.org/ontologies/50231"	"http://bioportal.bioontology.org/ontologies/46896"	"http://bioportal.bioontology.org/ontologies/44432"	""	
Term Source Version	""	""	""	""	""	"47845"	"50526"	"49709"	"50310"	"50280"	"46836"	"50231"	"46896"	"44432"	""	
Term Source Description	""	""	""	""	""	"National Center for Biotechnology Information (NCBI) Organismal Classification"	"Chemical Entities of Biological Interest Ontology"	"Ontology for Genetic Disease Investigations"	"Human Disease Ontology"	"Phenotypic Quality Ontology"	"Medical Subject Headings"	"BRENDA Tissue and Enzyme Source Ontology"	"Systematized Nomenclature of Medicine - Clinical Terms"	"Computer Retrieval of Information on Scientific Projects Thesaurus"	""	
INVESTIGATION
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INVESTIGATION PUBLICATIONS
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INVESTIGATION CONTACTS
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STUDY
Study Identifier	"E-GEOD-1919"
Study Title	"Transcriptional profiling of patients with osteoarthritis or rheumatoid arthritis, compared to normal controls. Patients are taking a mixture of NSAIDs, DMARDs (disease-modifying antirheumatic drugs), and steroids. Some samples are pools.[original title: Transcription profiling of human synovial samples from patients with osteoarthritis, rheumatoid arthritis vs controls treated with various drug regimes to characterise RA at the molecular level and to uncover key pathomechanisms]"
Study Description	"Synovial tissue collected during synovectomy. Six samples are from individual patients (individual), and nine are pooled samples from 2-4 individuals (pooled), some of mixed sex and drug regimen. Individual characteristics are indicated wherever possible. Note: Table 1 in the paper provides additional clinical characterization of the samples. [original description: Rheumatoid arthritis (RA) is a chronic, inflammatory joint disease of unknown etiology and pronounced inter-patient heterogeneity. To characterize RA at the molecular level and to uncover key pathomechanisms, we performed whole-genome gene expression analyses. Synovial tissues from rheumatoid arthritis patients were compared to those from osteoarthritis patients and to normal donors. Experiment Overall Design: Two disease conditions (rheumatoid arthritis and osteoarthritis) in comparison to normal donors were investigated. For the two disease groups samples derived from three individual patients and two pools of patients were hybridised.]"
Comment[Study Grant Number]	""
Comment[Study Funding Agency]	""
Study Submission Date	""
Study Public Release Date	"2007-11-11"
Study File Name	"s_E-GEOD-1919_study_samples.txt"
STUDY DESIGN DESCRIPTORS
Study Design Type	"in_vivo_design"	"disease_state_design"	"co-expression_design"	"transcription profiling by array"
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STUDY PUBLICATIONS
Study PubMed ID	"20858714"
Study Publication DOI	"10.1152/physiolgenomics.00004.2010"
Study Publication Author List	"Ungethuem U, Haeupl T, Witt H, Koczan D, Krenn V, Huber H, von Helversen TM, Drungowski M, Seyfert C, Zacher J, Pruss A, Neidel J, Lehrach H, Thiesen HJ, Ruiz P, Bläss S."
Study Publication Title	"Molecular signatures and new candidates to target the pathogenesis of rheumatoid arthritis."
Study Publication Status	"Published"
Study Publication Status Term Accession Number	""
Study Publication Status Term Source REF	""
STUDY FACTORS
Study Factor Name	"treatment3"	"diseasestate"	"treatment1"	"treatment2"
Study Factor Type	"compound"	"disease_state"	"compound"	"compound"
Study Factor Type Term Accession Number	""	""	""	""
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STUDY ASSAYS
Study Assay File Name	"a_E-GEOD-1919_GeneChip_assay.txt"
Study Assay Measurement Type	"transcription profiling"
Study Assay Measurement Type Term Accession Number	""
Study Assay Measurement Type Term Source REF	""
Study Assay Technology Type	"DNA microarray"
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STUDY PROTOCOLS
Study Protocol Name	"P-G1919-2"	"P-G1919-3"	"P-G1919-1"	"P-G1919-4"	"P-G1919-9"	"P-G1919-5"	"P-G1919-6"	"P-G1919-7"	"P-AFFY-6"
Study Protocol Type	"specified_biomaterial_action"	"specified_biomaterial_action"	"specified_biomaterial_action"	"specified_biomaterial_action"	"grow"	"nucleic_acid_extraction"	"labeling"	"hybridization"	"feature_extraction"
Study Protocol Type Term Accession Number	""	""	""	""	""	""	""	""	""
Study Protocol Type Term Source REF	""	""	""	""	""	""	""	""	""
Study Protocol Description	"non-steroidal anti-inflammatory drugs (NSAID)"	"disease modifying antirheumatic drugs (DMARD)"	"no treatment"	"disease modifying antirheumatic drugs (DMARD), non-steroidal anti-inflammatory drugs (NSAID), steroids"	"synovectomy"	"Total RNA was isolated using TRIzol Reagent (Invitrogen) followed by column based clean up (RNeasy, Qiagen)."	"The amplification and labeling of the RNA samples were carried out according to the manufacturer's instructions (Affymetrix, Santa Clara, CA). Briefly, total RNA was quantified by UV-spectroscopy and its quality evaluated by analysis on a LabChip (BioAnalyzer, AGILENT Technologies, Santa Clara, CA). In the presence of an oligo(dT)24 primer containing a T7 RNA polymerase promoter (Operon Biotechnology, Huntsville, AL, USA) five micrograms of total RNA were used for double-stranded cDNA synthesis (SuperScript transcriptase, Life Technologies, Inc., Carlsbad, CA). Labeled complementary RNA (cRNA) was prepared from double-stranded cDNA by in vitro transcription using the bioarray high yield RNA transcription kit (Enzo Diagnostics, Farmindale, N.Y., USA). After cleanup (Qiagen, Hilden, Germany), the biotin-labeled cRNA was fragmented by alkaline treatment (40 mM Tris-acetate (pH 8.2), 100 mM potassium acetate, and 50 mM magnesium acetate) at 94°C for 35 minutes."	"Fifteen micrograms of each cRNA sample was hybridized for 16 hours at 45°C to human expression Affymetrix HG U95Av2 GeneChip arrays. Following the hybridization arrays were washed and stained with streptavidin-phycoerythrin using a fluidics station in accordance with the Affymetrix protocol."	"Title: Affymetrix CEL analysis. Description: "
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Study Protocol Parameters Name Term Source REF	""	""	""	""	""	""	""	""	""
Study Protocol Components Name	""	""	""	""	""	""	""	""	"MicroArraySuite 5.0"
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STUDY CONTACTS
Study Person Last Name	"Ungethuem"
Study Person First Name	"Ute"
Study Person Mid Initials	""
Study Person Email	"uteung@onlinehome.de"
Study Person Phone	""
Study Person Fax	""
Study Person Address	"Core Center for Functional Genome Research, Charité University Hospital,  , Berlin, 10117, Germany"
Study Person Affiliation	"Charité University Hospital"
Study Person Roles	"submitter"
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