ONTOLOGY SOURCE REFERENCE
Term Source Name	"ArrayExpress"	"EFO"	"OBI"	"NCBITaxon"	"CHEBI"	"UO"	"BTO"	"XCO"	"DOID"	"PATO"	"MSH"	
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://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=UO"	"http://bioportal.bioontology.org/ontologies/50688"	"http://bioportal.bioontology.org/ontologies/50737"	"http://bioportal.bioontology.org/ontologies/50657"	"http://bioportal.bioontology.org/ontologies/50280"	"http://bioportal.bioontology.org/ontologies/46836"	
Term Source Version	""	""	""	"47845"	"50716"	"Jun 2010"	"50688"	"50737"	"50657"	"50280"	"46836"	
Term Source Description	""	""	""	"National Center for Biotechnology Information (NCBI) Organismal Classification"	"Chemical Entities of Biological Interest Ontology"	"Unit Ontology"	"BRENDA Tissue and Enzyme Source Ontology"	"Experimental Conditions Ontology"	"Human Disease Ontology"	"Phenotypic Quality Ontology"	"Medical Subject Headings"	
INVESTIGATION
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INVESTIGATION PUBLICATIONS
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STUDY
Study Identifier	"E-GEOD-2053"
Study Title	"Transcriptional profiling of synovial tissues from rheumatoid arthritis patients vs. normal controls. [original title: RAvs.ND]"
Study Description	"4 samples each of RA and normal synovial tissue. 6 of the 8 samples are actually pooled material from 2-4 patients with the same condition. When possible the age, sex, and list of current medications are indicated for each patient in each sample; current medications are listed by class as NSAID, DMARD, or steroid. Control samples were obtained from cadavers of accident victims. [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 to normal donors. Keywords: repeat sample Rheumatoid in comparison to normal donors were investigated. For both groups samples derived from individual patients and or pools of patients were hybridised.]"
Comment[Study Grant Number]	""
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Study Submission Date	""
Study Public Release Date	"2004-12-10"
Study File Name	"s_E-GEOD-2053_study_samples.txt"
STUDY DESIGN DESCRIPTORS
Study Design Type	"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."
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STUDY FACTORS
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STUDY ASSAYS
Study Assay File Name	"a_E-GEOD-2053_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-GSE2053-3"	"P-GSE2053-4"	"P-GSE2053-8"	"P-GSE2053-6"	"P-GSE2053-7"	"P-GSE2053-1"
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	"synovectomy"	"Total RNA was isolated using TRIzol Reagent (Invitrogen) followed by column based clean up (RNeasy, Qiagen)."	"20 µg of total RNA was primed with oligodT(12-18) and reverse transcribed with AMV (Roche) in the presence of alpha 33P-dCTP (Amersham Pharmacia Biotech)."	"The radioactive cDNA was purified using Sephadex columns, denatured and added to denatured salmon sperm and human placenta DNA as blocking reagents. To aid grid positioning during image analysis radioactively labelled 1 ng kanamycin cDNA was added to the complex probe. This mixture was added to 10 ml hybridisation buffer (1M NaCl, 1% SDS, 0.1xSSC) and hybridised overnight at 65°C and then washed three times for 20 min at 65°C (0.1% SDS, 0.1X SSC)."	"The filters were exposed for approx. 6 hours on Fuji BAS screens and signal intensities were read out using a Fuji Bas-1800 reader (Fuji Photo Film)."	"Signal intensities for every cDNA clone and background spots were determined using the Visual Grid software (GPC-Biotech, Munich). Raw intensities were background corrected by subtracting the local background (estimated block-wise) and normalised. ID_REF =   SIGNAL_RAW = raw intensity BKD_RAW = background intensity VALUE = normalised value"
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STUDY CONTACTS
Study Person Last Name	"Ungethuem"	"Ungethuem"	"Witt"
Study Person First Name	"Ute"	"Ute"	"Henning"
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Study Person Email	"uteung@onlinehome.de"	""	""
Study Person Phone	"+49 30 450576272"	""	""
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Study Person Address	"Core Center for Functional Genome Research, Charité University Hospital, , Berlin, Germany"	""	""
Study Person Affiliation	"Charité University Hospital"	""	""
Study Person Roles	"submitter"	""	""
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