In collaboration with the Genome Sciences Centre (GSC) in Vancouver, the Gene Array Facility at Vancouver General Hospital and the Biotechnology Research Institute in Montreal, the Treenomix team has recently developed cDNA microarrays to support transcript profiling experiments in spruce (Picea spp) and poplar (Populus spp).Our 2nd generation spruce 16.7K-unigene cDNA microarray is, to our knowledge, the largest cDNA microarray publicly available for any conifer species to date. Based on the high DNA sequence homology among conifer species, these arrays should be suitable for all Picea species, as well as the more distantly related Pinus genus and other members of the pine family [see Stasolla C. et al. (2003) Plant Physiology 131(1): 49].The 16.7K-microarray contains 16,740 unique cDNAs derived from eleven cDNA libraries representing foliage (4,805 clones), xylem (3,443), bark/phloem (3,931), roots (3,847) and phloem (714) of White spruce (P. glauca), Sitka spruce (P. sitchensis) and their hybrids. Some of these libraries were derived from stress-induced tissues treated with methyl-jasmonate or mechanical wounding [see Martin et al. (2002) Plant Physiology 129: 1003, Martin et al. (2003) Plant Physiology 132: 1586]. A variety of positive (e.g. human full-length cDNAs) and negative controls [e.g. human and E. coli Expressed Sequence Tags (ESTs), polyA DNA, pBluescript vector, 3x SSC and glass only spots], as well as an orientation marker, are included on each array.
We have also developed a poplar 3.3K-unigene cDNA microarray containing cDNAs derived from four cDNA libraries representing foliage (1,073), xylem (441) and phloem (1,803) of P. trichocarpa and P. trichocarpa x deltoides.This array contains the same set of controls as our spruce array.An expanded 15.5K poplar array is currently under development with printing of our first slides scheduled for spring 2004.This expanded array contains cDNAs derived from fourteen cDNA libraries representing insect-treated foliage and bark, nitrogen-depleted roots, elicitor-treated cultured cells, as well as xylem, phloem and floral tissues.
To support archiving and analysis of microarray data, we have established the Treenomix microarray database that is based on the open source BioArray Software Environment (BASE) platform [Saal L.H. et al. (2002) Genome Biology 3(8): software0003.1].With database support from the GSC and GenoLogics Life Sciences Software (based in Victoria), along with statistics expertise provided by Dana Aeschliman of Dr. Jenny Bryan's lab at UBC, we have incorporated customized R-script packages for quality control analysis, data normalization and identification of differentially expressed transcripts.In addition, we are also establishing links with the Treenomix EST database to facilitate detailed annotation and data mining.Via the Treenomix cDNA Microarray database, collaborators can also access detailed hybridization, scanning and image processing protocols, descriptions of array design, annotation for all cDNAs spotted on our cDNA microarrays, and quality control data related to array manufacture.
For further information regarding collaborative access to our cDNA microarray resources please contact Dr. Jörg Bohlmann or Dr. Steven Ralph.