Investigation Title Transcription profiling of peripheral blood monocytes from patients with systemic juvenile idiopathic arthritis during active and inactive disease
Comment[Submitted Name] Specific gene expression profiles in systemic juvenile idiopathic arthritis
Experimental Design co-expression_design disease_state_design transcription profiling by array
Experimental Design Term Source REF mo mo EFO
Comment[ArrayExpressReleaseDate] 2007-03-31
Comment[AEMIAMESCORE] 5
Comment[ArrayExpressAccession] E-MEXP-987
Comment[MAGETAB TimeStamp_Version] 2011-06-28 21:50:47 Last Changed Rev: 14857
Experimental Factor Name clinical_information
Experimental Factor Type clinical_information
Experimental Factor Term Source REF
Person Last Name Ogilvie
Person First Name Emma Mary
Person Mid Initials
Person Email emma.ogilvie@ucl.ac.uk
Person Phone 4.42077E+11
Person Fax
Person Address "45 Cleveland Street, London, London, W1T 4JF, UK"
Person Affiliation Immunology and Molecular Pathology
Person Roles submitter
Person Roles Term Source REF
Quality Control Type biological_replicate
Quality Control Term Source REF The MGED Ontology
Replicate Type
Replicate Term Source REF
Normalization Type
Normalization Term Source REF
Date of Experiment
Public Release Date 2007-03-31
PubMed ID
Publication DOI
Publication Author List "Emma Mary Ogilvie, Arshad Khan, Mike Hubank, Paul Kellam, and Patricia Woo"
Publication Title Specific gene expression profiles in systemic juvenile idiopathic arthritis.
Publication Status
Publication Status Term Source REF
Experiment Description Comaprison of PBMCs from patients with systemic juvenile idiopathic arthritis during active and inactive disease
Protocol Name P-MEXP-43833 P-MEXP-43832 P-MEXP-43877 Affymetrix:Protocol:Hybridization-Unknown P-AFFY-6 Affymetrix:Protocol:MAS4:ExpressionCall
Protocol Type specified_biomaterial_action nucleic_acid_extraction labeling hybridization feature_extraction bioassay_data_transformation
Protocol Description "PBMCs were obtained by density gradient centrifugation of blood over Lymphoprep® (Axis Shield), using endotoxin-free reagents. The PBMCs were resuspended in TRIZOL® (Invitrogen) at frozen at -80 °C." "1.Thaw frozen TRIzol lysate vial in 37°C water bath
2.Transfer to new eppendorf (autoclaved) and spin 12,000g, 10min, 4°C to remove insoluble material.
3.Transfer supernatant to new tube and leave at RT for 5min.
4.Add 0.2ml chloroform (per ml TRIzol) and shake by hand 15secs. Leave at RT 2-3mins.
5.Spin 12,000g, 15min, 4°C.
6.Transfer top aqueous phase to new tube. Keep lower phenol phase (contains DNA and protein) â freeze this at â80°C.
7.Add 0.5ml chloroform (per ml TRIzol) and shake 15secs. Leave at RT 2-3mins.
8.Spin 12,000g, 15min, 4°C.
9.Transfer aqueous phase to new tube and add 1 ul of glycogen and then add 0.5ml isopropanol (per ml TRIzol). Vortex and leave at RT for 10mins.
10.Spin 12,000g, 15min, 4°C.
11.Remove supernatant (keep) and add 1ml 75% ethanol (RT). Vortex to dislodge pellet.
12.Spin 7500g, 5min, 5°C.
13.Remove supernatant and spin in bench-top centrifuge 13,000rpm,1min.
14.Remove last traces of ethanol and air dry pellet 5min on bench.
15.Resuspend in 100μl DEPC-treated dH2O.
16.Quantitate RNA by spectrophotometry (A260/A280 programme)
2μl RNA in 498μl DEPC-dH2O.
Concentration (μg/μl) = A260 x 10
17.DNase treatment.
100μg RNA" 150μg RNA 200μg RNA
Protocol Parameters Amplification;Extracted product; Amount of nucleic acid labeled;Amplification;Label used;
Protocol Hardware
Protocol Software MicroArraySuite 5.0 MicroArraySuite 5.0 MicroArraySuite 4.0
Protocol Contact
Protocol Term Source REF mo mo mo mo
SDRF File E-MEXP-987.sdrf.txt
Term Source Name mo ArrayExpress The MGED Ontology mo EFO
Term Source File http://mged.sourceforge.net/ontologies/MGEDontology.php http://www.ebi.ac.uk/arrayexpress http://mged.sourceforge.net/ontologies/MGEDontology.php http://mged.sourceforge.net/ontologies/MGEDontology.php http://www.ebi.ac.uk/efo/
Term Source Version