title: University of Freiburg - Prochlorococcus microarray - MD4-9313 (MD4-9313a520062) version GC3.0
status: Public on Dec 31 2009
contact.city: Freiburg
contact.first: Claudia
contact.last: Steglich
contact.email: claudia.steglich@biologie.uni-freiburg.de
contact.address: Schaenzlestr. 1
contact.department: Biology
contact.country: Germany
contact.institute: University of Freiburg
contact.phone: 0049 761 203 6986
organism: Prochlorococcus marinus subsp. pastoris str. CCMP1986
  Prochlorococcus marinus str. MIT 9313
  Prochlorococcus phage P-SSM4
  Tiamatvirus PSSP7
manufacture_protocol: The MD4-9313 array (MD4-9313a520062) is a custom-made high density antisense Affymetrix array. This array detects labeled cDNA that is antisense to the original RNA. It contains probes for the genomes of two cyanobacterial strains, Prochlorococcus MED4 and Prochlorococcus MIT9313. The array contains probe sets to detect all predicted open reading frames with probe pairs approximately every 80 bases. For short open reading frames (ORF), the length of the gap was reduced to ensure a minimum of 11 probe pairs per ORF where possible. Probes were designed for intergenic regions longer than 35 bases and were spaced every ca 45 bases on both strands. For short intergenic regions the gap between probe pairs was reduced to ensure a minimum of 4 probe pairs where possible. For some short sequences, where insufficient high performance probes were designed using this approach, the best probes possible were designed with no regard for their spacing along the genome feature.  Note that the annotation was modified (compared to GPL5471) based on the annotation of Kettler et al. 2007, PLoS Genetics.