Title: Affymetrix CEL analysis. Description:
nucleic acid hybridization to array protocol
P-AFFY-3 GeneChip hybridization
normalization data transformation protocol
chips were normalized together using robust multichip average. Median polish was used for the probe level summary.
nucleic acid labeling protocol
Affymstrix GeneChip IVT Labeling Kit
nucleic acid extraction protocol
Total RNA was extracted from leaf using Qiagen Plant Mini Kit.
NL94-298 and NL94-145 two lines from the OSU switchgrass breeding population were used for this analysis. NL94-298 produced fewer tillers than NL94-145. Individual stems from several lines were harvested from field growing plants in the Agronomy field plots, Stillwater in August of 2011. Stems of the high tillering line had 2-3 phytomers, while the low tillering line had 1-2 phytomers. Cut ends of the tillers were placed in a beaker containing water. Vegetative buds from first phytomer were cut out using a sharp scalpel and immediately frozen in liquid nitrogen. Node regions from second phytomer were carefully cut out under a dissection scope and frozen in liquid nitrogen.