I have a question about maximizing the number of samples that can be applied on a single MiSeq run.
I am working with a single anaerobic bacterial species, in vitro, and want to analyze the transcriptome response to H2O2 and atmospheric oxygen.
I have access to a single MiSeq run with a max of 20 million reads (150 paired end reads) and want to include as many variable conditions as I can.
The minimum number of samples is 2 (a control point vs a stress point) allowing 10 million reads for each.
But if I wanted to increase the number of timepoints for example (T1hr, 6hr, 12hr etc) with different adapters: how many "samples" can be run using a single 20million flowcell that will still produce useful and reliable depth of data for each sample?
Another way of asking this is: What is the minimum number of total reads (150 paired end reads) that I would need for reliable comparative bacterial transcriptome analysis between a control condition and a stress condition?
Thank you in advance,