ONTOLOGY SOURCE REFERENCE
Term Source Name	"mo"	"EFO"	"ncbitax"	"efo.obo"	"The MGED Ontology"	"ArrayExpress"	"NCBITaxon"	"CL"	"DOID"	"CHEBI"	"BTO"	""	"OBI"	
Term Source File	"http://mged.sourceforge.net/ontologies/MGEDontology.php"	"http://www.ebi.ac.uk/efo/"	"http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html"	"/nfs/ma/ma-exp/GEOImportDownload/efo.obo"	"http://www.ebi.ac.uk/arrayexpress"	""	"http://bioportal.bioontology.org/ontologies/47845"	"http://bioportal.bioontology.org/ontologies/50456"	"http://bioportal.bioontology.org/ontologies/50310"	"http://bioportal.bioontology.org/ontologies/50447"	"http://bioportal.bioontology.org/ontologies/50231"	""	""	
Term Source Version	""	""	""	""	""	""	"47845"	"50456"	"50310"	"50447"	"50231"	""	""	
Term Source Description	""	""	""	""	""	""	"National Center for Biotechnology Information (NCBI) Organismal Classification"	"Cell Ontology"	"Human Disease Ontology"	"Chemical Entities of Biological Interest Ontology"	"BRENDA Tissue and Enzyme Source Ontology"	""	""	
INVESTIGATION
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INVESTIGATION PUBLICATIONS
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INVESTIGATION CONTACTS
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STUDY
Study Identifier	"E-GEOD-7669"
Study Title	"Transcription profiling of human synovial fibroblasts from rheumatoid arthritis and osteoarthritis patients"
Study Description	"Some patients are taking NSAIDs, and some are not. [original description: mRNA expression levels in synovial fibroblasts in 6 rheumatoid arthritis patients versus 6 osteoarthritis patients. Experiment Overall Design: Synovial tissue was obtained from open joint replacement surgery or Experiment Overall Design: arthroscopic synovectomy. Patients with RA or OA (n = 6 each for gene expression analysis and further patients for validation experiments) were classified according to the ACR criteria.]"
Comment[Study Grant Number]	""
Comment[Study Funding Agency]	""
Study Submission Date	""
Study Public Release Date	"2009-04-28"
Study File Name	"s_E-GEOD-7669_study_samples.txt"
STUDY DESIGN DESCRIPTORS
Study Design Type	"disease_state_design"	"transcription profiling by array"
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STUDY PUBLICATIONS
Study PubMed ID	"17594488"	"21474483"
Study Publication DOI	"17594488"	"10.1136/ard.2010.135665"
Study Publication Author List	"Dirk Pohlers, Andreas Beyer, Dirk Koczan, Thomas Wilhelm, Hans-Jürgen Thiesen, Raimund W Kinne"	"Geurts J, Vermeij EA, Pohlers D, Arntz OJ, Kinne RW, van den Berg WB, van de Loo FA."
Study Publication Title	"Constitutive upregulation of the transforming growth factor-beta pathway in rheumatoid arthritis synovial fibroblasts."	"A novel Saa3-promoter reporter distinguishes inflammatory subtypes in experimental arthritis and human synovial fibroblasts."
Study Publication Status	"journal_article"	"Published"
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STUDY FACTORS
Study Factor Name	"diseasestate"	"NSAID treatment"	"steroid treatment"	"methotrexate treatment"
Study Factor Type	"disease_state"	"treatment"	"treatment"	"treatment"
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STUDY ASSAYS
Study Assay File Name	"a_E-GEOD-7669_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-G7669-1"	"P-G7669-5"	"P-G7669-2"	"P-G7669-4"	"P-G7669-3"	"P-AFFY-6"	"Affymetrix:Protocol:ExpressionStat"
Study Protocol Type	"grow"	"specified_biomaterial_action"	"specified_biomaterial_action"	"nucleic_acid_extraction"	"labeling"	"feature_extraction"	"bioassay_data_transformation"
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Study Protocol Description	"The tissue samples were minced, digested with trypsin/collagenase P, and the resulting single cell suspension cultured for 7 days. Non-adherent cells were removed by medium exchange. SFB were then negatively purified using Dynabeads® M-450 CD14 and subsequently cultured over 2 passages in DMEM containing 100 ug/ml gentamycin, 100 ug/ml penicillin/streptomycin, 20 mM HEPES and 10% fetal calf serum (FCS, all from PAA Laboratories, Cölbe, Germany)."	"Synovial tissue was obtained from open joint replacement surgery or arthroscopic synovectomy at the Clinic of Orthopedics, Waldkrankenhaus “Rudolf Elle” (Eisenberg, Germany). Patients with RA or OA (n=6 each for gene expression analysis and further patients for validation experiments) were classified according to the ACR criteria."	"Synovial tissue was obtained from open joint replacement surgery or arthroscopic synovectomy at the Clinic of Orthopedics, Waldkrankenhaus “Rudolf Elle” (Eisenberg, Germany). Patients with RA or OA (n=6 each for gene expression analysis and further patients for validation experiments) were classified according to the ACR criteria."	"At the end of the 2nd passage, the SFB were starved with medium containing 1% fetal calf serum (FCS) for 72 h, to minimize stimulating effects by serum components. After washing with PBS, the cells were lysed with RLT buffer (Qiagen, Hilden, Germany) and frozen at -70°C. Total RNA was isolated using the RNeasy Kit (Qiagen) according to the supplier’s recommendation."	"RNA probes were labeled according to the supplier's instructions (Affymetrix, Santa Clara, CA, USA)."	"Title: Affymetrix CEL analysis. Description: "	"Title: Affymetrix CHP Analysis (ExpressionStat). Description: "
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Study Protocol Components Name	""	""	""	""	""	"MicroArraySuite 5.0"	"MicroArraySuite 5.0"
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STUDY CONTACTS
Study Person Last Name	"Beyer"
Study Person First Name	"Andreas"
Study Person Mid Initials	""
Study Person Email	"mail@a-beyer.de"
Study Person Phone	""
Study Person Fax	""
Study Person Address	"BIOTEC, Tatzberg. 47/49, Dresden, 01277, Germany"
Study Person Affiliation	"BIOTEC"
Study Person Roles	"submitter"
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