Comparing exposure time points of RNA-seq data of samples exposed to various treatments

Question

[abba647]

Hello, I have some RNA-seq data of samples exposed to specific treatments (n=3-4) at different doses and different time periods (24 hrs, 5 days, 10 days). The controls and treatments were run together for each time point. I want to look into signature changes across time points for each treatment compared to control, and also between the treatments. Initially I'd like to adjust for dosage, but later on I'd like to also look into differences across doses. I am planning on using DESeq2, but I'm not sure how to do time-series and the best practices. Any advice/guidance would be appreciated. Thank you!

Answer 1

[swbarnes2]

No one is going to spoon feed you how to do this. I recommend finding two tutorials, working through them both, then apply what you learned to your dataset. If you have specific questions, then you can ask those.

Answer 2

[Arby]

As swbarnes2 suggested, it might be difficult to get an exact answer. However, the DESeq2 user guide is very good, Look into their LRT model for "all time points" and their tutorial for your binary differential expression analysis