Comparison of Affymetrix and NuGEN amplification methods for HTA 2.0 microarray

Comparison of total RNA-seq and Affymetrix GeneChip(R) Human Transcriptome Array 2.0 analysis methods and Affymetrix GeneChip® WT PLUS Reagent and NuGEN Ovation® PICO WTA System V2 amplification methods for the detection of significant differentially expressed genes isolated from whole blood and brain RNA samples Affymetrix and NuGEN amplification methods are compared to determine which is most efficient, cost effective, and accurate in the detection of differentialy expressed transcript clusters on the HTA 2.0 microarray The optimum amplification microarray data is compared to total RNA-seq analysis of the same samples to determine which is the most efficient, cost effective, and accurate method of detecting differentially expressed genes Samples containing 100% blood, 67% blood/33% brain, 33% blood/67% brain, and 100% brain -derived RNA were amplified and hybridized onto HTA 2.0 microarrays. In R, limma was used to test for differential expression. These same samples were analyzed using total RNA-seq and results were also analyzed for differential expression. A subset of overlapping microarray and RNA-seq genes were compared for differential expression and log fold change ranges. Counts of differentially expressed genes were also compared from complete microarray and RNA-seq datasets as well as log fold change ranges for both methodologies Please note that Affymetrix and NuGEN datasets were normalized separately.