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All time series were normalized (subtraction) to the last time point of the baseline (TP3), thus this time point is always zero.
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No area normalized background subtraction using a second ROI outside of the thyroid ROI was performed for our analysis.
For the PCA, all variables were first normalized by subtraction of mean and division by standard deviation.
The gene expression data from PD were first log-transformed and normalized by subtraction of the mean value of all genes.
Using normalized cDNA subtraction as a transcript profiling tool to identify differentially expressed transcripts, we isolated several genes that may contribute toward understanding the mechanisms involved in meiosis and ovarian follicle differentiation in a mono-ovulatory species.
As phase scrambling can produce pixel intensities outside of the displayable range, pixel intensities of the scrambled images were linearly normalized (by subtraction of the minimum intensity and division by the sum of the minimum and maximum intensities) to within the displayable range.
For each gene, crossing point (Cp) values were determined from the linear region of the amplification plot and normalized by subtraction of the geometric mean of the crossing point (Cp) values for two housekeeping genes: ATP synthase 5B (and5B) and calnexin (CANX), identified by GeNorm analysis as the most stable housekeeping genes for this study.
In conclusion, using normalized cDNA subtraction as an alternative and complementary transcript profiling tool to DNA microarrays will help identify novel genes and low abundance transcripts, therefore achieving a more comprehensive global view of the transcriptome in the biological system studied.
Assay IDs for the specific primer/probe sets (Life Technologies, Carlsbad, CA, USA) are listed in Table S4 in Additional file 4. Samples were analysed as triplicates and normalized by subtraction of the sample mean Ct value from that of the mean Ct value of the housekeeping gene Gapdh.
After background subtraction, normalized spot intensity values were copied into Excel spreadsheets for statistical analysis.
Data were quantile normalized without background subtraction using Illumina BeadStudio software.
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