The microarray core facility in Washington University
Manufacture protocol
An antisense oligonucleotide array based on the published genome of S. pyogenes SF370 (Ferretti et al., 2001) was made at the Microarray Core Facility in the Genome-Sequencing Center at Washington University (GSC, http://genome.wustl.edu/groups/microarray/main_page/). A single 60–80 mer oligonucleotide was designed to hybridize to the putative transcripts from each annotated open reading frame using ‘TOP’ software that was created at the GSC. To reduce complexity, probes for rRNA, tRNA genes were not included. The oligonucleotides were synthesized by Illumina and were deposited onto a MWG epoxy microarray slide by custom Linear Servo Arrayer so that each slide included triplicates spots for each probe. Quality of the array was validated by hybridization with a Cyanine 5-labelled random nonamer (Hybchecker, Sigma) to ensure that the frequency of missed spots were less than 1.0% and by self-self hybridization using a single RNA sample to generate Cyanine 3- and Cyanine 5-labelled cDNAs, which were then co-hybridized on the slide. Slide batches were rejected if the average ratio of hybridization differed significantly from 1.0.
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