title: DSM PENa520255F Penicillium chrysogenum 14k v1.0
status: Public on Aug 28 2008
contact.city: Delft
contact.first: Marco
contact.middle: Alexander
contact.last: van den Berg
contact.email: Marco.Berg-van-den@DSM.COM
contact.address: PO Box 425
contact.country: Netherlands
contact.institute: DSM Anti Infectives
organism: Penicillium chrysogenum
description: Penicillium chrysogenum strain Wisconsin 54-1255
manufacture_protocol: Affymetrix Custom GeneChip program, 49-7875 format, 11μm features. 11 probe pairs per set. The CDF file is linked below as a supplementary file.
  GeneChip design Based on the genome sequence of Wisconsin54-1255, a proprietary GeneChip®, DSM_PENa520255F, was designed for DSM according to the Custom GeneChip® program by Affymetrix (Affymetrix, Inc., Santa Clara, CA). The chips of the 49-7875 format contain 11μm features. There are 11 pairs of 25-oligonucelotides in each probe set representing each of the approximately 13670 annotated ORFs and supplemented with genetic elements and a selection of large intergenic sequences of P. chrysogenum. The probe sequences were designed based on the region in the (predicted) coding sequence stretching from 650 to 4 nt, from the 3’ end. Typical Affymetrix control probe sets were included (B. subtilis, E. coli, Bacteriophage P1 and A. thalinana spike controls). For several known P. chrysogenum genes, separate 3’ end, middle and 5’ end probe sets were designed that allow monitoring the efficiency of the in vitro transcription reaction. In addition, 1551 probe sets were included to search for the presence of yet unpredicted ORFs within large sequences (>2500nt) between two predicted ORFs or genetic elements. For this, the ‘intergenic’ regions were split up in 800 nt fragments (skipping 300nt from each end) and probe sets were designed for both strands (coding and reverse complement) for the sequences stretching from 300-1100 (gn3, 494 sets); 1900-2700 (gn5, 177 sets) ; 3500-4300 (gn7, 44 sets); 5100-5900(gn9, 5 sets); 6700-7500 (gn11, 5 sets); 8300-9200 (gn13, 2 sets) and 10000-10800 (gn15, 2 sets) until the 300nt from the 5’end of the region. Intergenic regions on the border of two contigs were represented by two probe sets marked with A and B (i.e.. gn3A, gn3B and gn5A, gn5B).