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The pellets were kept at −80°C until further processing (genomic DNA preparation, PCR, and microarray hybridization, see below).
These motifs either represent false-positive predictions or might be related to genes that were not detected with significant values during DNA microarray hybridization (see below).
RNA was isolated from corollas of WT and ir- hd20 plants at 12 pm (6 h before the start of BA emission) and used for microarray hybridization (see Materials and Methods for a detailed description of the method and data analysis).
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Transcript expression levels were examined using DNase (Qiagen, Valencia, CA) treated total RNA from each of the three biological replicates used in microarray hybridizations (see Additional file 1 for methods).
The fragmented DNA was then diluted to a concentration of 13.4 ng/μl and denatured for 10 minutes at 95°C, after which two input fractions (approximately 250 ng each), serving as references in subsequent microarray hybridizations (see below), were collected and stored at −80°C.
Liver RNA was isolated from groups of male and female mice euthanized at each developmental time point and analyzed in seven sets of competitive microarray hybridization experiments (see Additional file 3A).
For further information about the hybridization, see the KTH microarray core facility webpage [ 26] (SOP 003 under 'Protocols'Protocols
For further information about the hybridization see SOP 003 at the KTH microarray core facility web site [ 32] under 'Protocols'Protocols
Overall, the expression patterns of all the 13 genes analyzed by sqRT-PCR were consistent with those by microarray hybridizations [see Additional file 11].
Please see Microarray hybridization and analysis for discussion of statistical methods used for genome-wide data.
One hippocampus of three animals per group (vehicle, vorinostat, tadalafil and the combination) was used for RNA extraction, Affymetrix microarray hybridization and data analysis (see Additional file 1: Additional methods).
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