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4) Why wasn't there a directly comparable DNA substrate to the RNA (21 nt) in subheading "Role of helicase activity in 5' Okazaki fragment processing"?
These results are now presented in subheading "DDB1 interacts with distinct DCAF proteins in a cell type specific manner" and can be found in Figure 10.
The combination of models, as described in Figure 1B and point 3 in subheading "Model selection", consists of having a different linear equation for distinct partitions of the data (for example one equation for each season).
The new data are presented in Figure 7 and discussed in subheading "ADF/cofilin-mediated disassembly of non-contractile actin filament bundles is important for maturation of ventral stress fibers".
However, since we do not yet fully understand why this is and how it relates to our existing framework, we have decided to not include these data into the current manuscript, but mentioned this result in subheading "The physiological constituents of the age-associated protein deposit include prion protein Sup35".
The PCA analysis further allows us to better understand variability across the cell population, as shown in the new analysis presented in subheading "Factor analysis" Figure 5 and Figure 6. Figure 7: This is a major thrust of the paper, in support of the notion that cells that are grouped by similar output have variable physiological parameters.
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This result was represented as Figure 5D in the revised manuscript, and explained in paragraph three, subheading "Effect of IREF-2 on viral RNA synthesis in infected cells" in the revised manuscript.
This result was newly added as Figure 5D in the revised manuscript, and explained in paragraph three, subheading "Effect of IREF-2 on viral RNA synthesis in infected cells".
More specifically, it is not clear how the decision in paragraph two, subheading "Modeling the effect of climatic factors on transcriptomic variation in different field environments" was implemented, as this can be carried out in many ways.
In paragraph four, subheading "Modeling the effect of climatic factors on transcriptomic variation in different field environments", it should be included that the BIC is calculated on the joint piecewise models; I suppose the number of parameters corresponds to the number of predictors summed over all models, or does it correspond to the number of unique predictors over all models?
We have included Ramachandran values in the Methods, subheading "Structure determination and refinement".
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