normalization data transformation protocol
GeneSpring GX (v. 7.3.1) was used for background subtraction and LOWESS normalization. ID_REF = VALUE = Lowess-normalized log2 ratio of expression (small fish/large fish) PRE_VALUE = Lowess-normalized ratio of expression (small fish/large fish)
array scanning protocol
Images were scanned on a GenePix 4200A scanner. Images were quantified using Genepix Pro software (version 6.1).
cDNA was hybridized according to Preventing Ozone Related Problems version of the the hybridization protocol described in Two-Color Microarray-Based Gene Expression Analysis (Agilent Technologies) in Agilent hybridization chambers.
cDNA was prepared from 0.5 ug mRNA using a SuperScript® Plus Direct cDNA Labeling System with Alexa Fluor® aha-dUTPs and labelled with either Alexa Fluor 555 or Alexa Fluor 647 according to the manufacturer's instructions.
nucleic acid extraction protocol
Total RNA extracted using Trizol following manufacturer's instructions. mRNA was extracted from total RNA using μMACS mRNA Isolation Kits – Small Scale according to the manufacturer's instructions.
Rainbow trout from the Lyndon strain were reared at Alma Aquaculture Research Station and fed ad libitum.