I have metadata, as shown in the figure. I want to compare treated vs. control within a single group only across all time points. I want to compare control from Group A to Treatment from Group A to get the fold change and p-value and store them in a separate file. Can anyone help me with how I can do that with the help of contrast or name arguments in DEseq2? How can I generate a design file.?

For setting up an appropriate design, please consult with a statistician or someone familiar with linear models in R. I have to reserve my time on the support site for software related questions.