title: 100428_GG_Bderm_SLH14081_expr
status: Public on Jun 01 2015
contact.city: Madison
contact.first: Gregory
contact.middle: M
contact.last: Gauthier
contact.email: gmg@medicine.wisc.edu
contact.state: WI
contact.address: 1550 Linden Drive
contact.department: Medicine
contact.country: USA
contact.institute: University of Wisconsin - Madison
contact.phone: 608-265-0429
organism: Blastomyces gilchristii SLH14081
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.
manufacture_protocol: 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