Hi, I am planning to check the difference of gene expression (including coding and non-coding genes) for RNA of a time course during induced differentiation of MSC (the mesenchymal stem cells). I have performed induction of two patient's clones and two clones of normal individuals. For each of the four clones, I reserved RNA at 10 time spots (Day0, Day4, Day7,......) during the differentiation course with triplication (3 wells for each time spot of each clone). I also did a non-induced control experiment of the four clones. So I have reserved quite a lot of RNA on my hand: [ 4 (two patient's clones and two normal clones) 10 (time spots) 3 (triplicates) * 2 (induced and non-induced) = 240 ] and sequencing all of them would be too expensive. May I have your suggestions on how to design a RNA-seq experiment for the materials I had? Thank you very much in advance!
