i am planing to do very soon mRNAseq on different combinations of multiple knockouts (KO) in a set of genes. In total i have 15 different knockouts and i would like to analyse the differential expression of each of them compared to WT (wild type).
I have at my disposal 3 different clones of each of these knockouts as biological replicates. So in total there are 15 x 3 (KO samples) + 3 (WT samples) = 48 samples ( in the case i dont consider technical replicates ).
- Whats the most reasonable way to distribute the samples in the flow cell ? In other words, to be cost effective without compromising the data quality, whats the maximum number of samples to be put in a single lane ?
Is it necessary to include technical replicates ? In this case i would have to deal with about 100 samples !
I am new in the field of NGS and couldnt find an appropriate answer to my concern. Thanks a lot.