Transcript Profiling of Plant Tissues

All of the libraries were comprised of a single organ or tissue, and the majority of libraries were developed by pooling samples collected at different points along a time course, along the diurnal cycle, at several stages of differentiation or from different treatments (Supplemental data 2 and [58 ]). Treatments known to affect plant physiology were applied to saplings (young trees) aiming to stimulate different transcript profiles. These treatments included N and P fertilization as well as stem girdling. Three libraries were made from whole root systems of very young spruce seedlings, produced through tissue culture, grown in sterile growth media. Most of the libraries were derived from one genotype (pg-653), however four libraries were comprised of two or more genotypes. The secondary xylem collected from saplings (library GQ007) was comprised of the entire sampling of woody tissues collected from seedlings; however, only the differentiating partly-lignified secondary xylem was collected from mature trees as previously described [16 (link)]. The secondary xylem tissues were collected by first gently separating the bark from the underlying wood and scraping the soft tissues inward of the cambial area. The secondary phloem of mature trees was collected by gently scrapping the inner surface of the bark with a scalpel blade. All tissue samples were frozen in liquid nitrogen and then stored at -80°C until RNA extraction immediately upon removal from the tree, seedling or tissue culture vessel.