title: WashU_crypto_ver2_array
status: Public on Sep 04 2010
contact.city: Lynchburg
contact.first: Michael
contact.middle: S
contact.last: Price
contact.email: msprice2@liberty.edu
contact.state: VA
contact.address: 1971 University Blvd.
contact.department: Biology & Chemistry
contact.country: USA
contact.institute: Liberty University
contact.phone: 434-592-7277
organism: Cryptococcus neoformans
manufacture_protocol: The v1.0 array represents an effort to generate an array useful for all of the currently predicted genes in serotype D. This set includes all the C. neoformans genes that were manually annotated by The Institute for Genome Research using a combination of automated gene prediction, homology, and EST data (Loftus et al, 2005). The set also includes all genes predicted by the TWINSCAN software (Korf, Flicek, Duan, and Brent, 2001; Tenney, Brown, Vasquez, Lodge, Doering, and Brent, 2004) that are not already included in the TIGR set. The gene list generated from these two sources was used to choose a set of oligos for each gene using ArrayOligoSelector, and the final oligo for each gene was chosen to primarily optimize homology to genes predicted in serotype A, and secondarily by proximity to the 3' end of the coding sequence. Oligonucleotide sequences, sources, physical characteristics, and TIGR annotations (where applicable) are in a spreadsheet linked under Array Specific Information at the left. The TWINSCAN database used in this work may be similarly accessed.
  The revised array includes all of the content from the previous array, as well as new probes designed for:
  * 3,075 serotype A genes that did not match (≤2 mismatches) any probe in the previous probe set
  * 477 serotype D genes (B3501 or JEC21) that did not match (≤2 mismatches) any probe in the previous probe set
  * 48 mating locus genes – the array now represents both mating types of both serotypes