title: Agilent-030142 ARO_Ophir_Egrandis_expression_18k
status: Public on May 01 2015
contact.city: Rishon Le-Zion
contact.first: Ron
contact.last: Ophir
contact.email: ron@volcani.agri.gov.il
contact.address: Hamacabim St.
contact.department: Fruit Tree Sciences
contact.country: Israel
contact.institute: Agricultural Research Organization - the Volcani Center
organism: Eucalyptus grandis
description: Custum made Agilent expression array of 18K probes, designed based on eucalyptus version 1 array of 44K probes. A detailed description is described in a previous study (Abu-Abied M et al. Plant journal). Briefly, 71,208 contigs published in Novaes et al., 2008 study was run against public databases databases [e.g. NR (http://www.ncbi. nlm.nih.gov/), Arabidopsis (http://www.arabidopsis.org), proteins of other plants at TAIR (http://www.arabidopsis.org), PlantGDB (http://www.plantgdb.org) and UniRef (http://www.ebi.ac.uk) at EBI] to define the orientation. Orientation of contigs that had no hit was defined by either existence of poly-A or by discovering the ORF. Probes from each contig was designed by Tm optimizing using OLIGOWIZ (Wernersson and Nielsen, 2005). In version a subset of 18K probes were taken with a first priority for the probes that were found statistically significant in Abu-Abied M et al. Plant journal.
manufacture_protocol: http://www.genomics.agilent.com/literature.jsp?pgId=AG-PG-6&contentType=User+Manual&languageSelectionDD=English&page=1