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I am preparing total RNA samples from rat brain tissue to look at differential gene expression (single read, 1x50). HighSeq3000 allows for 300 million reads. I am wondering if I can use one lane for 23 samples, with the assumption that each sample will yield approximately 12 million reads.
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Take a look at this thread for some background. Since HiSeq 3000 runs patterned flowcells you should consider this. Best option would be to dual index your samples and clean your libraries of adapter contamination.
12M reads per sample is not enough for DE with a mammalian genome.
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