Mitochondrial DNA quantitative polymerase chain reaction (qPCR) data.
MITO_DNAdata.frame with 30 rows and 8 columns:
integer; unique 5 digit identifier of all samples collected for an acute test/sample collection period. All samples collected during that period will have the same BID.
factor; the sex of the rat with 2 levels "Female" and "Male".
factor; exercise training group. Either "SED" (sedentary) or the number of weeks of training ("1W", "2W", "4W", "8W").
factor; unique combination of sex (first letter)
and timepoint.
numeric; mean of the duplicate \(\Delta C_T\) values from each sample.
numeric; standard error of mean_delta_CT.
numeric; mean_delta_CT values centered on the
mean of the "F_SED" exp_group.
numeric; \(2^{-\Delta \Delta C_T}\) values.
Quantification of mitochondrial DNA (mtDNA) was performed and described by Amar, et al. (https://doi.org/10.1101/2023.01.13.523698). Briefly, real-time quantitative PCR was performed in duplicate for each of the scWAT samples selected for -omics analysis. The \(2^{-\Delta \Delta C_T}\) method (https://doi.org/10.1006/meth.2001.1262) was then applied to estimate the relative expression of the mitochondrial D-loop. Since both target (D-loop) and internal control (\(\beta\)-actin) were amplified in the same well, \(\Delta C_T\) was calculated as the mean of (\(C_{T,\beta-loop} - C_{T,\beta-actin}\)) for each sample. Then, \(\Delta \Delta C_T\) values were obtained by subtracting each \(\Delta C_T\) value by the mean \(\Delta C_T\) of the sedentary female group (the calibrator).
Amar, D., Gay, N. R., Jimenez-Morales, D., Beltran, P. M. J., Ramaker, M. E., Raja, A. N., Zhao, B., Sun, Y., Marwaha, S., Gaul, D., Hershman, S. G., Xia, A., Lanza, I., Fernandez, F. M., Montgomery, S. B., Hevener, A. L., Ashley, E. A., Walsh, M. J., Sparks, L. M., … The MoTrPAC Study Group (2023). The mitochondrial multi-omic response to exercise training across tissues. BioRxiv. https://doi.org/10.1101/2023.01.13.523698
Livak, K. J., & Schmittgen, T. D. (2001). Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2−ΔΔCT Method. Methods, 25(4), 402–408. https://doi.org/10.1006/meth.2001.1262
head(MITO_DNA, 10)
#> # A tibble: 10 × 8
#> bid sex timepoint exp_group mean_delta_CT SE_delta_CT delta_delta_CT
#> <dbl> <fct> <fct> <fct> <dbl> <dbl> <dbl>
#> 1 90245 Female SED F_SED -6.10 0.127 0.181
#> 2 90248 Female SED F_SED -6.48 0.0819 -0.207
#> 3 90252 Female SED F_SED -6.28 0.133 -0.00769
#> 4 90265 Female SED F_SED -6.82 0.103 -0.540
#> 5 90266 Female SED F_SED -5.70 0.00273 0.574
#> 6 90559 Female 1W F_1W -5.96 0.0392 0.320
#> 7 90560 Female 1W F_1W -6.03 0.145 0.251
#> 8 90564 Female 1W F_1W -5.72 0.0179 0.561
#> 9 90567 Female 1W F_1W -6.36 0.0705 -0.0864
#> 10 90571 Female 1W F_1W -6.99 0.103 -0.710
#> # ℹ 1 more variable: relative_expr <dbl>