Lets say i have RNA sequence data from three groups: \
1 = Control_untreated (healthy cells), \
2 = Case_untreated (diseased cells),  \
3 = Case_treated (diseased cells with siRNA knockdown against a gene suspected of causing disease by altering the expression profile)

Question 1:
Would i be able to use a PCA plot to summarise the RNA expression profiles and see if the treatment drags the case group towards the control group?

Question 2 (if Q1=yes): 
I know oxford nanopore systems are not ideal for RNA-seq yet due to lacking dept. But since im interested in comparing just a summery of the expression profiles would it be possible to use it for generating the data i need?

Question 3 (if Q1=yes): 
Is it possible to do something similar for an DEU or DTU analysis?
1. Yes you can. You can also try TSNE or ICA
2. If you just care about expression, nanopore is not a good choice. Traditional RNA-seq or microarray is better. Nanopore is designed for long-read sequencing and has advantages in calling variants such as splicing isoform, gene fusion. Quantifying the expression level is not the aim of nanopore.
3. Yes