title: ULaval/CRH_Tomato_200_v1.0
status: Public on Jan 07 2009
contact.city: Québec
contact.first: Jean-François
contact.last: Dubuc
contact.email: jean-francois.dubuc.1@ulaval.ca
contact.address: 2440 boul. Hochelaga
contact.country: Canada
contact.institute: Université Laval
organism: Solanum lycopersicum
description: The array consists of 8 sub-grids (2 meta-rows, 4 meta-columns) which are present in three replicates.
manufacture_protocol: This cDNA microarray from tomato was produce using spotted PCR fragment. The array was particularly enriched in genes associated with photosynthesis, carbon and nitrogen metabolism, transduction signals, stress and defense mechanisms and housekeeping functions. Primers for 120 genes were chosen using the software Primer3 (Rozen and Skaletsky, 2000). Genes or EST sequence were accessed via the National Center for Biotechnology Institute (NCBI). PCR product sizes were ranging from 200 to 800 bp. The PCR reactions were performed with the Expand high fidelity (Roche Diagnostics, Laval, QC, Canada) and PCR TGradient Thermocycler (Biometra, Goettingen, Germany). Each PCR product was purified with Montage PCR filter units (Millipore, Billerica, MA) and sequenced (SUCOF, QC, Canada) to confirm the authenticity of the amplified fragment. Amplification products of known genes were evaporated with Savant speedvac concentrator (Thermo Fisher Scientific, Waltham, MA), resuspended in 50% (v/v) dimethyl sulfoxide in double distilled water and arrayed with the VersArray ChipWriter Pro (Bio-Rad, Mississauga, ON, Canada) on GAPS II coated slides (Corning, Lowell, MA). All the genes present on the array were printed at least in six replicates in order to take into consideration of possible technical variations. The SpotReport Alien cDNA Array Validation System (Stratagene, La Jolla, CA), consisting of two artificial Alien sequences, was printed on the array. The print quality and the detection sensitivity of the arrays was access by the addition of these external and negative controls. A 700 pb fragment of the green fluorescent protein (GFP) was added to the microarray as a positive control.