Comparisons Of RNA Quality Control In Postmortem Brain And Implications To Microarray Analysis of Gene Expression.

Mary Atz; Marquis P. Vawter; Hiro Tomita; Jun Li; Kevin Overman; Simon Evans; Prabhakara Choudary; David Walsh; Manuel O. Lopez-Figueroa┬┐; Rick Myers; Stanley J. Watson; E.G. Jones; Huda Akil; William E. Bunney, Jr.
Society for Neuroscience 34th Annual Meeting. 2003.


We have assembled a cohort of mood disorder subjects and controls for analysis of gene expression as part of a large multi-site effort to analyse the molecular profiles in multiple brain regions. As part of this work, we reported the broad effects of pH and agonal factors on microarray analysis of gene expression (Li et al., 2004; Tomita et al., 2004) in pathways related to stress and oxidative phosphorylation. We also found that RNA integrity was related to agonal factors and proposed using the average correlation index (ACI, Tomita et al., 2004) to evaluate RNA integrity. This initial work was performed with U95A Affymetrix chips. We now report data from additional samples run on U133A Affymetrix chips. Comparisons of RNA integrity (Auer et al., 2003) with cRNA yields from in vitro transcription, microarray clustering results, and microarray quality control data are presented. From this iterative work emerges criteria for 'acceptable' and 'outlier' samples and chips in microarray analyses. Consistent with prior reports, RNA integrity, agonal factor, and pH influence gene expression profiling in postmortem brain.