ONTOLOGY SOURCE REFERENCE Term Source Name "CHEBI" "BTO" "OBI" "EFO" "NCBITAXON" "ERO" "UO" "DOID" Term Source File "http://data.bioontology.org/ontologies/CHEBI" "http://data.bioontology.org/ontologies/BTO" "http://data.bioontology.org/ontologies/OBI" "http://data.bioontology.org/ontologies/EFO" "http://data.bioontology.org/ontologies/NCBITAXON" "http://data.bioontology.org/ontologies/ERO" "http://data.bioontology.org/ontologies/UO" "http://data.bioontology.org/ontologies/DOID" Term Source Version "78" "20" "21" "111" "2" "13" "42" "399" Term Source Description "Chemical Entities of Biological Interest Ontology" "BRENDA Tissue and Enzyme Source Ontology" "Ontology for Biomedical Investigations" "Experimental Factor Ontology" "National Center for Biotechnology Information (NCBI) Organismal Classification" "Eagle-I Research Resource Ontology" "Units of Measurement Ontology" "Human Disease Ontology" INVESTIGATION Investigation Identifier "Inv_001" 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 "GSE36700" Study Title "Gene expression profiles in synovial biopsies from patients with arthritis" Study Description "GeneChip¨ Human Genome U133 Plus 2.0 Arrays (Affymetrix UK Ltd., High Wycombe, UK) were hybridized in monoplicates with 10 µg biotinylated cRNA, using synovial biopsy samples obtained in 4 patients with SA [seronegative arthritis, spondylarthritis] (based on the presence of psoriasis or x-ray evidence of sacro-iliacal joint involvement), 5 patients with MIC [microcrystalline arthritis, gout], based on the identification of urate or calcium pyrophosphate crystals in the synovial fluid, 7 patients with RA [rheumatoid arthiritis] (ACR 1987 criteria), 4 patients with SLE [lupus] (ACR criteria) and 5 patients with OA [osteoarthiritis] (based on x-ray evidence of osteoarthritis)" Comment[Study Grant Number] "" Comment[Study Funding Agency] "" Study Submission Date "2012-03-22" Study Public Release Date "2012-03-27" Study File Name "s_GSE36700.txt" STUDY DESIGN DESCRIPTORS Study Design Type "" Study Design Type Term Accession Number "" Study Design Type Term Source REF "" STUDY PUBLICATIONS Study PubMed ID "17469140" Study Publication DOI "10.1002/art.22578" Study Publication Author List "Nzeusseu Toukap A, Galant C, Theate I, Maudoux AL, Lories RJ, Houssiau FA, Lauwerys BR." Study Publication Title "Identification of distinct gene expression profiles in the synovium of patients with systemic lupus erythematosus." 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_GSE36700_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 "GPL570" STUDY PROTOCOLS Study Protocol Name "RNA extraction" "labeling" "nucleic acid hybridization" "data collection" "normalization data transformation" "data transformation" "sample collection" Study Protocol Type "RNA extraction" "labeling" "nucleic acid hybridization" "data collection" "normalization data transformation" "data transformation" "sample collection" Study Protocol Type Term Accession Number "" "" "" "" "" "" "" Study Protocol Type Term Source REF "" "" "" "" "" "" "" Study Protocol Description "Total RNA was extracted from synovial biopsy tissue using the Nucleospin RNA II extraction kit (Macherey-Nagel, DŸren, Germany), which included DNase treatment of the samples." "Labeling of RNA (complementary RNA [cRNA] synthesis) was performed according to a standard Affymetrix procedure (One-Cycle Target Labeling kit; Affymetrix UK, High Wycombe, UK). Briefly, total RNA was first reverse transcribed into single-stranded complementary DNA (cDNA) using a T7-Oligo(dT) Promoter Primer kit (Affymetrix UK) and Superscript II reverse transcriptase. RNase H was then added together with Escherichia coli DNA polymerase I and E coli DNA ligase, followed by a short incubation with T4-DNA polymerase in order to achieve synthesis of the second-strand cDNA. The purified double-stranded cDNA served as the template for the in vitro transcription reaction, which was carried out overnight in the presence of T7-RNA polymerase and a biotinylated nucleotide analog/ribonucleotide mix. At the end of this procedure, the biotinylated cRNA was cleaned and fragmented by a 35-minute incubation at 95¡C." "GeneChip Human Genome U133 Plus 2.0 arrays (spotted with 1,300,000 oligonucleotides informative for 47,000 transcripts and originating from 39,000 genes; Affymetrix UK) were hybridized overnight at 45¡C in monoplicate cultures with 10 ?g cRNA. The slides were then washed and stained using the EukGE-WS2v5 Fluidics protocol on the GeneChip Fluidics Station (Affymetrix UK)." "The slides were scanned on a GeneChip Scanner 3000." "For the initial normalization and data analysis steps, data were retrieved using Affymetrix GCOS software. The frequency of positive genes on each slide was 48Ð55%. After scaling of all probe sets to a value of 100, the amplification scale was reported to be between 1.1 and 2.5 for all slides. The signals yielded by the poly(A)-RNA, hybridization, and housekeeping controls (GAPDH 3?:5? ratio <2) were indicative of the good quality of the amplification and hybridization procedures." "Statistical analyses of the microarray data were further performed using GeneSpring software (Agilent, Palo Alto, CA). For each slide, scaled data were normalized to the 50th percentile value for each chip and to the median value for each gene. The data were assessed by analysis of variance (ANOVA) with or without Benjamini-Hochberg corrections for multiple comparisons." "Patients: All patients with SLE met the American College of Rheumatology (ACR; formerly, the American Rheumatism Association) revised classification criteria for SLE (5), all were female, and the mean age was 32 years (range 19Ð40 years). All SLE patients had active articular disease at the time of synovial tissue sampling, and none had received immunosuppressive therapy; some of the SLE patients were receiving nonsteroidal antiinflammatory drugs. All patients with RA met the ACR classification criteria for RA (6) and all had early (<1 year's duration) active disease at the time of tissue sampling. Among the patients with RA, 2 were female and 5 were male, and the mean age was 51 years (range 37Ð69 years). In these patients, the mean C-reactive protein (CRP) level was 25 mg/liter (range 9Ð96 mg/liter), and the mean Disease Activity Score in 28 joints (including the CRP) (7) was 5.08 (range 3.76Ð5.82). None of the RA patients had received any treatment, except with nonsteroidal antiinflammatory drugs. Among the patients with OA, 5 were female and 1 was male, and the mean age was 63.2 years (range 51Ð73 years). The diagnosis of seronegative arthritis was based on the presence of psoriasis or x-ray evidence of sacro-iliacal joint involvement). The diagnosis of microcrystalline arthritis was based on the identification of urate or calcium pyrophosphate crystals in the synovial fluid. Tissue: Synovial biopsy tissue (15Ð20 synovial samples per patient) was obtained by needle arthroscopy of the affected knee of patients with systemic lupus erythematosus (SLE n = 4), patients with rheumatoid arthritis (RA n = 7), patients with osteoarthritis (OA n = 5), patients with seronegative arthritis (SA, n = 4) and patients with microcrystalline arthritis (MIC n = 5). For each patient, 4Ð6 synovial samples were snap-frozen in liquid nitrogen and stored at ?80¡ for later RNA extraction. The same amount of tissue was also kept at ?80¡ for future immunostaining experiments on frozen sections. The remaining material was stored in formaldehyde and paraffin-embedded for conventional optical evaluation and immunostaining of selected cell markers." 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 ""