title: FGRc UPR-RRP/RUM D. Hansenii Array
status: Public on Mar 15 2008
contact.city: San Juan
contact.first: Sandra
contact.last: Pena de Ortiz
contact.email: sandra@hpcf.upr.edu
contact.state: PR
contact.address: Gandara Ave., JGD Bldg. Rooms 108, 204
contact.department: Department of Biology
contact.country: Puerto Rico
contact.web_link: http://fgrc.hpcf.upr.edu
contact.institute: University of Puerto Rico
contact.phone: 787-764-0000 ext 7957
organism: Debaryomyces hansenii
manufacture_protocol: Whole genome mRNA sequences from D. hansenii were downloaded in FASTA format from GenBank (http://www.ncbi.nih.gov) and saved into a text file. Sequences in text format were downloaded to the eArray web design application from Agilent Technologies (Santa Clara, CA) for probe design.  Two probes per target were designed in the sense orientation with a 3’ bias using base composition methodology as recommended by the manufacturer for gene expression arrays.  Using comparative genomics, probes were aligned to other yeast sequences and were classified according to their similarities: highly similar, similar, some similarities, weakly similar, and no similarities, all based on sequence homologies.  Probes were tested for self-complementarities, specificity, and cross reactivity. The best probes were used for generating a custom microarray arranged in an 8 X 15K format using a randomized lay out.  Each array included 12,640 probes, 60 bp of length, 459 positive (spike-in) controls, and 77 negative control probes distributed across the array.  Positive controls were used as a quality control of the cRNA synthesis, labeling, and hybridization steps, whereas negative controls were included to estimate fluorescence background and background variance.