RNA-seq data analysis to detect dosage effect or proportional increase/decrease in expression across a series

Question

[nancy]

Hi- I have some RNA-seq data from a series of 4 isogenic strains (0,1,2,3), differing in their copy number of a single gene. I would now like to identify those genes whose expression changes across these samples in proportion to the copy number of the gene of interest.

For e.g., in the series 0,1,2,3, what genes show proportional increase in tpm/fpkm as we go from 0 to 3, and what genes show proportional decrease.

I imagine I should be able to model this in DESeq2, but am unable to exactly figure out how. Any pointers/help will be appreciated. Open to using methods other than DESeq2 too, if needed.

Thanks in advance.

[Mark]

How many biological replicates do you have for each strain? The edgeR manual has an example on how to analyse time series data.

https://www.bioconductor.org/packages/devel/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf

Checkout section 3.3. This is their hypothetical experimental design:

Treat           Time
Sample1 Placebo 0h
Sample2 Placebo 0h
Sample3 Placebo 1h
Sample4 Placebo 1h
Sample5 Placebo 2h
Sample6 Placebo 2h
Sample7 Drug 0h
Sample8 Drug 0h
Sample9 Drug 1h
Sample10 Drug 1h
Sample11 Drug 2h
Sample12 Drug 2h

Note that for each time point, they have two independent samples for each condition. This is the bare minimum number of biological replicates neccessary to perform DE analysis (whether Deseq2 or edgeR it doesn't matter).