The microarray experiment included five internodes with three biological replicates, used 15 Affymetrix Genechips in total.
In addition, transcripts (contigs) preferentially transcribed in HS (low MFA) juvenile wood in a single microarray experiment included many other secondary cell wall genes, such as 4CL, CCoAOMT, chitinase-like, SAMS, PPBG, AGP4, GRP2, PRP, etc (data not show).
The samples for microarray experiment included 3 vegetative stages (mature leaf, 7-day-old seedling, and their roots), 11 reproductive stages (P1 P6 and S1 S5; representing panicle and seed developmental stages, respectively), and 3 abiotic stress conditions, i.e. cold, salt, and dehydration.
The samples for the microarray experiment included three vegetative stages (mature leaf, 7 days old seedling and their roots), 11 reproductive stages (P1-P6 and S1-S5; repanicleing pandcle and seed developmental stages, respectively) and three abiotic stress conditions, i.e. cold, salt, and dehydration.
Some basic issues of microarray experiments, including experimental design, data analysis, and gene validation, are also discussed.
JR and JL performed all microarray experiments including CGH and gene expression.
KYY and MRP performed the microarray experiments including all statistical and bioinformatic analyses.
GAP and DAM designed the microarray experiments including expression analysis pipeline, GAP participated in writing the manuscript.
RM, SCS and SM carried out all DNA microarray experiments including RNA isolation and preparation of cDNA.
AT wrote the paper, interpreted the results, performed the in silico and statistical analyses, and conducted the microarray experiments, including the cultivation of the plants.
