I want peoples opinions on this sort of approach to RNA-Seq.
If I am running an RNA-Seq study and we have 4 treatments:
and we have 4 time points, T0,T1,T2,T3
The original plan was to take 3 biological replicates( 1 plant as a biological replicate) for each treatment over each time point - which is the norm in DGE RNA-Seq experiments. However is it deemed inappropriate if we were to take 2x3 plants at the same time point and treatment, and pool 2 of the 6 plants into each of the 3 biological replicates?
The idea behind this, is to get a more accurate estimation of differential gene expression between treatments over time points,whilst minimising statistical variance. Obviously plants in treatments will be stronger/ weaker than others and will be behaving different, despite a 2 week week acclimation period to control treatment.
Please let me know if this pulling of tech reps into biological reps would be frowned upon or cause bias? And also if it would in fact make a more sound RNA Seq DGE experiment and analysis.
Thanks very much.