title: Porphyromonas gingivalis W83 array
status: Public on May 30 2008
contact.city: Seoul
contact.first: Ji-Hoi
contact.last: Moon
contact.email: prudence75@khu.ac.kr
contact.address: 1 Hoeki-Dong, Dongdaemoon-Ku
contact.department: Oral Microbiology
contact.country: South Korea
contact.institute: School of Dentistry, Kyung Hee University
contact.phone: +82-2-961-0598
organism: Porphyromonas gingivalis
manufacture_protocol: The whole genome of 1,909 genes of P. gingivalis W83 (GenBank accession no. NC_002950) was submitted to NimbleGen System Inc. (Madison, WI, U.S.A.) for microarray design and manufacture using maskless, digital micromirror technology. Five replicates of the genome were included per chip. An average of 19 different 60-base oligonucleotides (60-mer probes) represented each genes in the genome. 60-mer probes were selected such that each probe had at least three mismatches compared to all other 60-mers in the target genome. A quality control check (hybridization) was performed for each array, which contained on-chip control oligonucleotides. The arrays were analyzed using an Axon Gene Pix 4000B scanner with associated software (Molecular Devices Corp., Sunnyvale, CA). Gene expression levels were calculated with NimbeScan Version 2.3 (NimbleGen). Relative signal intensities for each gene were generated using the Robust Multi-Array Average algorithm. The data were processed based on quantile normalization method using the R package.