Hi there, I am currently doing a project for my masters degree on some pre-existing time course RNASeq data of covid progression in a cell line of caco-2. I have time points at 0h, 1h, 2h, 4h, 7h, 12h, 24h and 48h as well as control data at time points 4h, 12h and 48h, for all timepoints there are 3 replicates for the data. I am just wondering what would be the best way to include the control data in my study as i do not have control replicates for each of the timepoints?

Sorry if the question is a bit trivial but I have been doing some research and I have been having some trouble finding the best way to proceed.

Thanks for any help!

You could fit a spline trend with design matrix treatment+spline. Then it won't matter than the control and treatment times don't match up. See the edgeR User's Guide for a trend example.

Another trend example is given here https://f1000research.com/articles/12-684/v2 but it's more complex than you need.