Hallo we have an RNA-Seq experiment and I would like to ask for your suggestion about how to best sequence the samples
We are working on mammalian cell lines (human or mouse) and would like to sequence samples for a time-series analysis
we have four conditions and four time-points each in triplicates. In total we have 48 samples. We have a nextSeq 500 and we'll use the high kit with ~400M reads.
As we would like to reach a good coverage we decided to split the samples on two (or maybe three cell lines). If we take three flow-cells there won't be a problem, as I can just put one replicate of each of the three on one flow-cell.
My question is what would be best to do, if using only two flow-cells? we would than like to put 24 samples per flow cell. I was thinking to run it like this-
Would it make sense, or do I miss some important factors?