385K whole genome gene expression design for Blastomyces dermatititidis SLH14081 (including mitochondrion, sequence from Broad Institute, plus 3 probes from customer supplied lamba sequence). 9587 initial CDS seequences, 9583 with probles, 10 probe per sequence except for 12 seqs with fewer, position_weight=50; 4 copies of each probe on the array, empty features filled with randomly generated probes of comparable length and G+C content to act as controls for nonspecific binding. Arrays were prepared using Maskless Array Synthesizer (MAS) technology
Description
385K whole genome gene expression microarrays (Roche NimbleGen, Inc., Madison, WI) were custom designed for B. dermatitidis using the annotated sequence of strain SLH14081 (9,587 genes; www.broadinstitute.org). At the time these arrays were designed, SLH14081 was the only sequenced and annotated genome avaiable for Blastomyces dermatitidis. A total of 9,583 genes (nuclear and mitochondrial) were represented on each array in quadruplicate with 9,571 genes having a probe-set comprised of 10 unique oligonucleotide probes; 12 genes had less than 10 unique oligonucleotide probes. Oligonucleotide probes with sufficient specificity were unable to be designed for a mitochondrial laglidadg endonuclease (BDBG_17014), mitochondrial ATP synthase F0 subunit 8 (BDBG_17017), mitochondrial NADH dehydrogenase subunit 5 (BDBG_17032), and a predicted protein (BDBG_03106). Empty features on the array were filled with randomly generated probes with similar length and G+C content as the NimbleGen internal controls.
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