Assessment of RNA-seq Sample Preparation Methodology

The goal of this study was two-fold, to determine if common purification techniques have any effect on downstream differential expression analysis and to evaluate combinations of alignment and differential expression software for reliability. To this end, blood was collected from three individuals and pooled during and after extraction. After pooling and mixing was completed, samples were divided into three aliquots for testing. The first aliquot was a control and not purified or concentrated. It was diluted to produce samples of varying concentrations for testing. The second aliquot was diluted to 20 ng/uL and used to test six different variations on the AMPure XP bead purification procedure. The last aliquot was also diluted to varying concentrations of 60, 30, and 9.6 ng/uL and... (for more see dbGaP study page.)