A-AFFY-58 - Affymetrix Custom Array - MD4-9313 v1 [MD4-9313a520062]

Organism
Cyanophage P-SSM4;Cyanophage P-SSP7;Prochlorococcus marinus str. MIT 9313;Prochlorococcus marinus subsp. pastoris str. CCMP1986
Description
The MD4-9313 array is a custom-made high density Affymetrix antisense array. It contains probes for the genomes of two cyanobacterial strains, Prochlorococcus MED4 and Prochlorococcus MIT9313 (Rocap et al. 2003), as well as two ds-DNA phages that infect Prochlorococcus MED4 the podovirus P-SSP7 and the myovirus P-SSM4 (Sullivan et al. 2005). For the Prochlorococcus strains, this array contains probe sets to detect predicted open reading frames with probes spaced every ca 80 bases along the length of each ORF as well as for intergenic regions (>35 bases) spaced every ca 45 bases on both strands. Probe spacing was decreased in short ORFs and intergenic regions to achieve at least 11 probes per ORF and 4 probes per intergenic regions where possible. 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 to be detected) and a mismatch probe (containing a single base change at the center of the probe). This is an antisense array and is designed for protocols that generate and use labeled cDNA or cRNA sequences that are antisense to the original RNA.


PSSP7 probesets in version 1 of the array were developed from provisional genome sequences and should not be considered correctly mapped to the PSSP7 genome.


Rocap et al. (2003). Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 424(6952):1042-1047.


Sullivan et al. (2005). Three Prochlorococcus cyanophage genomes: Signature features and ecological interpretations. PLoS Biology 3(5):790-806.
Version
1.0
Provider
John Aach (aach@receptor.med.harvard.edu);Affymetrix, Inc. (support@affymetrix.com)
Links
Experiment E-TABM-91
Files
Array DesignA-AFFY-58.adf.txt