title: Histoplasma_capsulatum_G217B_WGTA_026583
status: Public on Aug 12 2011
contact.city: San Francisco
contact.first: Mark
contact.last: Voorhies
contact.email: mark.voorhies@ucsf.edu
contact.state: CA
contact.address: 513 Parnassus, S472
contact.department: Microbiology and Immunology
contact.country: USA
contact.institute: University of California
organism: Histoplasma capsulatum
manufacture_protocol: Arrays were designed based on the Washington University Genome Sequencing Center (GSC) Histoplasma capsulatum strain G217B genome assembly as of 11/30/2004. Degenerate sequence and transposable elements were removed from the assembly using RepeatMasker with default parameters and the repeat families determined by the GSC. The remaining sequence was tiled with 50mer probes at an average frequency of one probe every 60 base pairs. Probe spacing was adjusted to minimize variation in melting temperature, and a subset of probes were truncated to optimize synthesis, in collaboration with CombiMatrix. The number of arrays used to tile a given contig was minimized, and the location of tiling probes was randomized within a given array. In addition, each array contained a common set of control probes, viz.: quality control (QC) and negative control (NC) probes designed by CombiMatrix; positive control probes tiling the genomic loci and non-genic flanking sequence of TEF1(P40911), TYR1, and CBP1(AF006209); and probes specific to a spike-in control sequence. Arrays were synthesized by CombiMatrix.