The results of principal component analysis (PCA) of microarray data and representative K-means profiles of tissue-/stage-specific gene expressions are shown in Figure 4. Three major regions of dispersion are found: A) genes specifically expressed in roots, B) genes expressed specifically in stems and leaves and C) genes specifically expressed in seeds.
In order to validate the microarray data, we selected representative genes and analyzed their expression using qRT-PCR.
To validate the microarray data, we selected representative genes regulated by Alethea and/or salinity for analysis by reverse transcription (RT) PCR.
To corroborate the mouse microarray data, we analysed representative host response genes by real time RT-qPCR in the same RNA samples, using the GAPDH housekeeping gene as an internal control.
To validate the microarray data, a number of representative differentially expressed genes were selected to be individually studied by Real-Time PCR (n = 5 10 per group).
To verify the microarray data, we selected 30 representative genes from different gene categories.
Moreover, in agreement with the microarray data, the protein levels of representative components of the Electron Transport Chain (ETC), particularly those belonging to complexes IV and V, were reduced in the Stat3 C/C cells.
Validation of the microarray data was performed by qPCR using three representative candidates of under-represented, over-represented and normally-represented genes from the control group and TP3.
In addition, we validated our microarray data by measuring mRNA levels of representative genes (Scd2, Srebf1, Lpin1, Pparg, Cyp7a1, and Abcb11) using quantitative real time-PCR (Figure S2 and S3).
The microarray data used [ 24, 25] are representative of C. elegans microarray data: bias curves very similar Figure 4 are observed when microarray data averaged over 553 microarray experiments [ 32] are compared to the limited EST data [ 22] or the entire C. elegans EST database [ 30, 31].
