title: A human ImmunoChip cDNA microarray provides a comprehensive tool to study immune responses.
abstract: DNA microarray technology has developed rapidly in recent years and has become an essential tool, providing novel approaches to biomedical research. In this paper, we describe a self-designed ImmunoChip cDNA array for immunological research. With a comprehensive selection of genes of interest, we can focus on key signalling pathways and molecular mechanisms at relatively low cost compared to commercial platforms which are usually targeted at global screening of gene expression. To validate the efficiency of the ImmunoChip, we studied T helper cell polarization to functionally distinct subsets (Th1 and Th2). We also developed a tool for quality control of cDNA microarrays that assesses the technical quality of an ImmunoChip. The information produced with the quality control tool is shown to be valuable for extracting correct information from cDNA microarrays. Gene expression measurements with ImmunoChip are in agreement with the results obtained using oligonucleotide microarrays and with published quantitative RT-PCR data. The ImmunoChip provides reliable measurements and gives new insights into various aspects of human immune responses.
authors.affiliation: Turku Centre for Biotechnology, FIN-20521, Turku, Finland. tuomas.nikula@btk.fi
authors.forename: T
authors.initials: T
authors.lastname: Nikula
authors.forename: A
authors.initials: A
authors.lastname: West
authors.forename: M
authors.initials: M
authors.lastname: Katajamaa
authors.forename: T
authors.initials: T
authors.lastname: Lönnberg
authors.forename: R
authors.initials: R
authors.lastname: Sara
authors.forename: T
authors.initials: T
authors.lastname: Aittokallio
authors.forename: O S
authors.initials: OS
authors.lastname: Nevalainen
authors.forename: R
authors.initials: R
authors.lastname: Lahesmaa
mesh_terms: D018076:DNA, Complementary; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation / Q000276:immunology; D006801:Humans; D007111:Immunity, Cellular; D007376:Interleukin-2 / Q000502:physiology; D015847:Interleukin-4 / Q000502:physiology; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D011786:Quality Control; D018417:Th1 Cells / Q000276:immunology / Q000378:metabolism; D018418:Th2 Cells / Q000276:immunology / Q000378:metabolism; D016212:Transforming Growth Factor beta / Q000502:physiology
chemical_list: D018076:DNA, Complementary; D007376:Interleukin-2; D016212:Transforming Growth Factor beta; D015847:Interleukin-4