I am a PhD student planning on doing an RNAseq experiment looking for gene expression changes in Salmon fish. I am planning on 8 tanks of salmon in total. 4 tanks will be infected with a disease and 4 tanks will be healthy. I am planning on taking samples from the fish at 9 different time points. I plan to take Gill, Kidney, Liver and Blood samples.
Per time point I plan on taking 2 fish from each tank. Therefore 8 healthy and 8 unhealthy fish. 16 in total. Taking 4 samples from each fish would equal 64 tissue samples per time point. So at the end of all my timepoints I would end up with 576 sample, 288 healthy samples and 288 unhealthy samples . This is where Im getting really confused. Do i have enough replicates.
How do I know my sample size is big enough, can someone recommend a power analysis software.
What should I ask for when looking for quotes from companies. As budget is an issue I need to keep that in mind. I know I can pool libraries but not samples.
What depth and number of reads is recommended for looking at gene expression.
How many samples can be put on each Lane.
If anyone can help me i would be really thankful.