title: [AsprgDTUa520520F] Custom Affymetrix Aspergillus Chip DTU_3Aspergillus_45K_v1.0
status: Public on Feb 10 2008
contact.city: Kgs. Lyngby
contact.first: Mikael
contact.middle: R
contact.last: Andersen
contact.email: mr@bio.dtu.dk
contact.address: Søltofts plads, bygn 223
contact.department: BioCentrum-DTU
contact.country: Denmark
contact.institute: Technical University of Denmark
organism: Aspergillus niger
  Aspergillus oryzae
  Aspergillus nidulans
description: Type: CustomExpress. Feature size: 11-micron. Format: 49-7875
manufacture_protocol: Initial probe-design was done using the OligoWiz 2.0 software (Nielsen, 2003, Wernersson, 2005) from CDS sequences of predicted ORFs from the genome sequences of A. nidulans FGSC A4 (Galagan, 2005), A. niger ATCC 1015 (Baker, 2006) and A. oryzae RIB40 (Machida, 2005).  For each gene, a maximum of 11 non-overlapping perfect match probes were calculated using the OligoWiz standard scoring of cross-hybridization, melting temperature, folding, position preference and low complexity. A 3' position preference for the probes was included in the computations. The probes were designed separately for each genome. Pruning of the probe sequences to comply with Affymetrix recommendations was done by removing duplicate probe sequences and shortening probes that were not possible to synthesize in full length. Also included on the chip iss a number of Affymetrix standard controls, custom controls, an A. oryzae EST-collection (courtesy of Novozymes A/S) and probes for ORFs from the S. coelicolor A3(2) (Bentley, 2002) genome.