I want to do a RNA-seq for 30 cancer patients that can be divided into two groups of 150. Each patient have normal and cancerous tissue paired. The problem is that we have money ONLY for 36 samples in total.
I was thinking, at first, to use 3 normals for each group of 15 as a way to use my samples in DE analysis. But then it ocurrured to me: Why not pool 5 normal tissues, 3 times each, so all normal tissue will be represented with less RNA-seq?
Like: Group 1 - 15 cancer samples - 3 pools of 5 normal paired Group 2 - 15 cancer samples - 3 pools of 5 normal paired
We were planning 100million reads paired-end, which is the standard in our institution.