title: MIT-Chisholm Lab Prochlorococcus and cyanophage microarray - MD4-9313 (MD4-9313a520062)
status: Public on Sep 07 2007
contact.city: Haifa
contact.first: Debbie
contact.last: Lindell
contact.address: Technion City
contact.department: Department of Biology
contact.country: Israel
contact.institute: Technion - Israel Institute of Technology
organism: Prochlorococcus marinus subsp. pastoris str. CCMP1986
  Prochlorococcus marinus str. MIT 9313
  Prochlorococcus phage P-SSM4
  Tiamatvirus PSSP7
description: Array format - Midi; Synthesis area - 8.1 mm; Feature size - 18 micron
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, as well as two dsDNA phages that infect Prochlorococcus MED4 – the podovirus P-SSP7 and the myovirus P-SSM4. For the Prochlorococcus genomes, 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. For the phage isolates, probe pairs were designed across the genomes for both strands at an approximate interval of 90 bases. Probes are 25 bases long and each probe pair consists of a perfect match probe (identical to the sequence) and a mismatch probe (containing a single base change at the center of the probe).