genotype: Maize inbred line 3681-4 age: 10d after sowing tissue: mesocotyls
The total RNA was extracted by the TRIzol method (Invitrogen, USA). Mesocotyls were ground in liquid nitrogen, and 50-100 mg of frozen tissue was transferred into a tube with 1 ml TRIzol. Next, RNA was isolated, dried and dissolved in 50 µl DEPC-H2O. RNA quality and concentration were determined by 1.0% agarose gel electrophoresis and spectrophotometry.
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45℃ on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Gene expression data from maize mesocotyl
The data were analyzed with GCOS software (Microarray Suite version 5.0, MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.