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To estimate repeatability (broad sense heritabilities at the individual level), the mixed model was refit with genotype, experiment and genotype*experiment as random terms in the model (Supplementary file 3).
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To evaluate the quality of genotype experiments, we compared genotype calls that were generated using the Affymetrix Gtype 4.0 software between blood and normal experiments.
Genotype experiments were performed by Affymetrix, Santa Clara CA, following their standard protocol.
On the contrary, genes in NSCB were significantly differentially expressed in genotype experiments, indicating notable activities and biological function of nitrogen-containing compounds in plants of different genotypes.
All genotype experiments were made at least in duplicate, with quality control of automated allele calling by two independent operators blind to phenotype.
All genotype experiments were made at least in duplicate, with quality control of automated allele calling by two independent operators blind to phenotype (0% replicate error rate).
Regulatory rewiring was revealed by the variability of genes' expression: pathway genes and transcription factors (TFs) were significantly differentially expressed under different conditions (such as terpenoids biosynthetic genes in tissue experiments and E2F/DP family members in genotype experiments).
For instance, a member of E2F/DP family (E2Ff, AT3G01330) was more specific to genotype experiments; whereas a member of C2H2(Zn) family (ID1, AT1G25250) was more typical to tissues.
We were given access to the validated HapMap genotyping data for these samples only after we had finished the main genotyping experiment (287 SNPsles/50 SNPs), and after we had sent a file of our genotyping results to McGill University.
We have demonstrated DNA amplification in this device, using an external peristaltic pump, and the PCR product was used with a DNA bioelectronic sensor chip (Motorola e-Sensors™) for genotyping experiment.
Analysis of four independent databases reveals that a considerable fraction of mutation in functional genes can be described by a few CMCs regardless of gene identity or population stratification in the genotyping experiment.
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