Quality control parameters on a large dataset of regionally dissected human control brains for whole genome expression studies

Abstract

In this recent paper, we assessed the quality of RNA in post-mortem brain from healthy individuals as part of our on-going work to create a database of whole genome expression. We have received comments that the values for the RNA Integrity Number (RIN) that we report here are much lower than those reported for comparable samples in other laboratories. Upon closer examination, we now believe this is most likely due to differences in the RNA preparation kit and RNA isolation methods. Most RNA kits, including the popular RNAeasy kit, encourage the loss of small or degraded RNA species. However, in this paper we used the miRNAeasy kit which specifically allows for the preservation of short RNA species, as we are also interested in characterizing miRNA later on with transcriptome sequencing. When small RNA is present, as in our case, the RIN algorithm generates lower RIN values. This means that the RIN values in our paper, and the reported levels of association with covariates and other measures of array performance, are not directly comparable with those reported in other studies where different RNA isolation kit has been employed.