The Design of a Gene Chip for Functional Immunological Studies on a High-Quality Control Platform

• Published in: Annals of the New York Academy of Sciences Vol. 1005; no. 1; pp. 284 - 287
• Main Authors: WAUKAU, JILL, JAILWALA, PARTHAV, WANG, YOUMIN, KHOO, HUOY-JII, GHOSH, SOUMITRA, WANG, XUJING, HESSNER, MARTIN J.
• Format: Journal Article
• Language: English
• Published: Oxford, UK Blackwell Publishing Ltd 01.11.2003
• Subjects: array; B cell; Chemokines - genetics; Cytokines - genetics; expressed sequence tags; gene chip; Matarray; Oligonucleotide Array Sequence Analysis; Quality Control; T cell
• ISSN: 0077-8923; 1749-6632
• DOI: 10.1196/annals.1288.044

: We have created an immunology‐related microarray chip containing primarily known genes with well‐studied functional properties. By looking at known genes rather than expressed sequence tags, we hope to gain a better understanding of immunological pathways and how they work. The immunology gene chip contains genes from the following functional categories: T cell genes; B cell genes; dendritic cell genes; chemokine and cytokine genes; apoptosis genes; cell cycle genes; cell interaction genes; general hematology and immunology genes; and adhesion genes. We have also developed a novel three‐color cDNA array platform in which arrays are directly visualized before hybridization, which allows us to select only high‐quality chips for our experiments. In an effort to provide quantitative quality control for each array element as well as the entire chip, we have developed Matarray, a software package for image processing and data acquisition. With Matarray, we have built a quantitative data filtering and normalization scheme that has proved to be more efficient than the existing methods. The list of immunology chip genes is available from the authors.