This study showed considerable variation in RIN values among RNA samples. Sixty-seven per cent of the variation resides in differences among extractions from the same tissue blocks and most of the remaining variation is unexplained by the available covariate information. We found that pH is the most important post-mortem factor influencing RIN-based RNA integrity, a result consistent with previous studies (Hardy et al. 1985; Mexal et al. 2006; Chevyreva et al. 2008; Monoranu et al. 2009; Durrenberger et al. 2010). Samples with very low pH values (ranging from 5.42 to 5.90) were responsible for the positive correlation seen between pH and %P (and also RIN). However, when these low pH samples were removed from the analysis we no longer observed any significant correlation. This may in part explain contradictory observations regarding the effect of pH on RNA integrity and sample performance on arrays (Hardy et al. 1985; Monoranu et al. 2009; Birdsill et al. 2010) and confirms the findings of a recent, but smaller study on control brain tissue (Tomita et al. 2004; Sherwood et al. 2011).
