Hi, I am new to bioinformatics and am running the DESeq2 pipeline on a 8 murine RNA-seq samples. I am having some trouble understanding how best to set up my design formula. The basic structure of my experiment is as follows:

I have 8 samples: Samples 1 and 2 (biological replicates) : Cell line A; treated with vehicle Samples 3 and 4 (biological replicates): Cell line A; treated with drug Samples 5 and 6 (biological replicates): Cell line B; treated with vehicle Samples 7 and 8 (biological replicates): Cell line B; treated with drug

The primary analyses I would like to perform are as follows: a) To determine whether certain genes display significant differential changes in expression in response to drug between the two cell lines (comparing drug/vehicle between cell lines A and B) b) To determine whether there are differences in gene expression at baseline (between vehicle conditions of cell line A and B)

I am happy to split this into two separate analyses if needed. Please advise and let me know how I should set up my design formula. I appreciate your help! Please let me know if you need any additional information.

It sounds like you could use a design of ~condition + condition:treatment which will give you a baseline difference between condition A and B as well as condition specific treatment effects for the treated vs vehicle for A and B separately.