A randomly selected nucA construct (pLp_3093sNuc) was used as the control for all other samples in REST calculations, and expression ratios were calculated accordingly.
Note that introducing these parameters primarily aims to simplify the calculations and expressions of the paper.
The DEDMS contains data access, data verification, data statistics, index calculation, and index expression components.
Cufflinks and Cuffdiff (Trapnell et al., 2012) were used for the reads per kb of exon model per million mapped reads (RPKM) calculation and differential expression analyses.
The details of expression calculation and differentially expressed gene detection were shown in Supplementary Note 3. The distribution of time to TMRCA (the most recent common ancestor) between two alleles in an individual can be related to the history of population size fluctuation.
The log ratios for the eight methionine hybridizations were imported into Genstat® 11.1 for statistical analysis (ANOVA) and calculation of expression estimates and standard errors for each of the four bulks.
Numerical calculation examples were solved, and good agreement was confirmed between the numerical calculation and the analytical expression mentioned above.
To also validate our slender body approach (i.e., demagnetization field calculation and magnetic load expression) for large deflections, we analytically solve for the large (postbuckling) rotational deformation of slender beams.
The pragmatic approach often compromises mathematical rigor, but offers instead expediency of calculation and elegance of expression.
Finally, NormFinder fits data to a mathematical model, which allows comparison of intra- and intergroup variation and calculation of expression stability.
