Can i use PCA to summarise RNA expression profiles before and after treatment?

Question

[antonhomilius]

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?

Answer 1

[shiyang_bio]

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

[antonhomilius]

Thanks a lot!