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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.
The data were analyzed using ΔΔCt calculations and expression of all genes was normalized against the mouse housekeeping gene, HPRT.
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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.
We combined this with a comprehensive analysis of mitochondrial and nuclear gene expression patterns, co-expression calculations and transcription factor binding sites.
We subsequently analyzed the transcriptomes using three approaches: gene expression clustering, co-expression calculations, and transcription factor binding site analysis (Fig. 1).
Gene expression clustering, co-expression calculations and analysis of transcription factor binding sites provide insights into nuclear transcription regulation of OXPHOS, suggesting regulation of the system as a whole rather than regulation of specific complexes.
Calculation of the R0 and expression of tandem constructs, demonstrated that the red-shifted pairs display a relatively high FRET efficiency, which can be detected by FLIM or acceptor photobleaching.
The RMA algorithm was used to perform background subtraction, normalisation and expression calculation (output in the log2 scale).
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.
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