Equation (3), present in the supplemental note 1 in Supplementary file 1, was implemented using a custom R script for the actual un-mixing procedure.
A young time point to compare aged cells to was selected and processed as described in the supplemental note 3 in Supplementary file 1.
A simple correction step accommodating for the specific protein losses caused by the presence of the beads was applied to the relevant data, and is explained in the supplemental note 2 in Supplementary file 1.
To infer the high-level directional networks and find causal relations, six data analysis steps were undertaken, as expanded upon below in the supplemental note 4 in Supplementary file 1.
(A ) The directed and clustered transcriptome network consists of 3631 edges, connecting 1241 nodes in 8 clusters (see Figure 6 figure supplement 1 and supplemental note 4, in Supplementary file 1, for further details).
In the Supplemental Notes, he quotes [586] and [587] but neither of the papers of Davies and Robinson, despite the fact that in response to their writing to me after the preprint, I added a Note Added in Proof to [586] referencing their work.
Mathematical un-mixing rests on the idea that a system of linear equations can be solved when (i) the number of equations is equal to the number of unknowns and (ii) these are independent (see supplemental note 1 in Supplementary file 1 for terminology, explanation, and validation of the method).
A sensitivity analysis was performed to determine the optimal sparsity of the network and the cut-off for the partial correlation among transcript profiles, through which we established that the network was a robust representation of the datasets (supplemental note 4 in Supplementary file 1, Table S7, Figure 6 source data 1).
Following the un-mixing of the data, should the resulting data contained 'unsolvable' entries (see supplemental note 1 in Supplementary file 1), a data quality criteria was applied: at least five time points per time trace (0 72 hr) should be solvable, otherwise the protein or transcript was removed from the dataset.
This corrected measure shows rather strong (P < 0.0003) increase in diversity of mtDNA deletions with age (Supplemental Note 3), which fits the 'fast' expansion scenario (Fig. 1B).
