Today I submitted two QuantSeq 3′ mRNA-Seq libraries to the UChicago Functional Genomics Core for sequencing. Each library has 28 samples and will be sequenced on a separate 50bp SE HiSeq 4000 lane. For one library, I quantified the finished PCR products for each sample using Qubit and checked the quality using Bioanalyzer HS before pooling them myself. For the other library, I am letting the sequencing center pool the samples by estimating concentrations using qPCR. This is more expensive per sample (and slows down decision making as I’m not doing the QC myself), so I want to compare the two libraries and see if I can achieve fairly even sequencing with just Qubit. You can see my lab notebook and protocols here.