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All samples were compared to controls in triplicate, with one of three hybridizations involving a dye reversal.
Following microarray hybridization and analysis, 86.7% of all coding sequences included on AppChip2 could be detected during our experiments, and 150 genes were significantly differentially expressed in vivo when their level of expression was compared to that seen in vitro, with a FDR of 4.25% over the course of three hybridizations: 72 of these were up-regulated, while 78 were down-regulated.
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The films consisted mainly of two hybridizations, N sp2C and N sp3C bonds, but the fraction of N sp3C bonds decreased with increasing N content.
The replicate embryo pools were analyzed in two sets of dye-swaps making a total of four hybridizations.
A total of two hybridizations were conducted.
The design consists of four hybridizations of non-amplified material and eight hybridizations of amplified material.
This resulted in a set of six hybridizations.
Two separate experiments of six hybridizations each were conducted with each liverpairing having one dye-flip.
Two technical replicates were produced for each biological replicate, for a total of eight hybridizations.
A total of six hybridizations were performed in three experiments, using a cDNA microarray of 18613 soybean cDNAs.
Excel (Microsoft) was used to determine correlation coefficients between pairs of reference sample data of eight hybridizations.
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