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Series GSE19821 Query DataSets for GSE19821
Status Public on Jan 28, 2010
Title Rheumatoid arthritis and anti-TNF treatment
Organism Homo sapiens
Experiment type Expression profiling by array
Summary In 15 patients with rheumatoid arthritis the baseline expression (t=0) of type I IFN-regulated genes was determined in peripheral blood cells (PAXgene) using cDNA-microarrays and compared to levels one month after (t=1) anti-TNF treatment (infliximab). Therefore, we used 43K cDNA microarrays from the Stanford Functional Genomics Facility (http://microarray.org/sfgf/) printed on aminosilane-coated slides containing ~20.000 unique genes. Only one batch of arrays was used for all experiments. First DNA spots were UV-cross linked to the slide using 150-300 mJoules. Sample preparation and microarray hybridization were performed as described previously (1,2). Data storage and filtering was performed using the Stanford Microarray Database (http://genome-www5.stanford.edu//) as described previously. 1. van der Pouw Kraan TC, Wijbrandts CA, van Baarsen LG, Voskuyl AE, Rustenburg F, Baggen JM et al.: Rheumatoid arthritis subtypes identified by genomic profiling of peripheral blood cells: assignment of a type I interferon signature in a subpopulation of patients. Ann Rheum Dis 2007, 66: 1008-1014. 2. van der Pouw Kraan TC, van Baarsen LG, Rustenburg F, Baltus B, Fero M, Verweij CL: Gene expression profiling in rheumatology. Methods Mol Med 2007, 136: 305-327. Abbreviations: - Bnrs are the different patients analyzed - PAX or Paxgene indicates the total RNA was isolated from peripheral blood obtained in PAXgene tubes - CRS: common reference sample: We made a common reference that consisted of a mixture of mRNAs isolated from 11 different cell lines (Perou CM, Jeffrey SS, van de RM et al. Distinctive gene expression patterns in human mammary epithelial cells and breast cancers. Proc Natl Acad Sci U S A. 1999; 96:9212-9217) supplemented with RNA from rheumatoid synovial tissue, fibroblasts, and activated peripheral blood mononuclear cells (PBMCs). - PMT: photomultiplier tube: the sensitivity/intensity of the scanner can be adjusted to prevent spot saturation.
Compound Based Treatment: anti-TNF (infliximab)
 
Overall design reference_design
 
Contributor(s) Verweij C
Citation(s) 20096109
Submission date Jan 10, 2010
Last update date Dec 30, 2021
Contact name Lisa G.W. van Baarsen
E-mail(s) E.G.vanBaarsen@amc.uva.nl
Phone +3120-5665707
Fax +3120-5669756
Organization name EULAR & FOCIS Center of Excellence
Department Div. of Clinical Immunology and Rheumatology
Lab Dept. of Experimental Immunology Academic Medical Center
Street address Meibergdreef 9
City Amsterdam
ZIP/Postal code 1105 AZ
Country Netherlands
 
Platforms (3)
GPL9869 SMD Print_1015 Homo sapiens
GPL9870 SMD Print_1060 Homo sapiens
GPL9871 SMD Print_1066 Homo sapiens
Samples (30)
GSM494867 B142 RA TNF t=0 PAXgene vs CRS red 80 PMT
GSM494868 B129.2 RA TNF t=0 PAXgene vs CRS red 80 PMT
GSM494869 B154 RA TNF t=1 PAXgene vs CRS 40 PMT
Relations
BioProject PRJNA122147

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE19821_RAW.tar 7.7 Mb (http)(custom) TAR
Processed data included within Sample table
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