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

Description of the data used in the analysis.

(a) Scatter plot for total RNA samples with linear regression line of RIN numbers for pH. Plot shows the effect of pH on RIN number for RNA samples isolated from 13 region of control brain tissue. Test p-values is test p-value = 1.0 × 10−4, r-value = 0.145. Including the low pH values of < 5.9. (b) Scatter plot for total RNA samples with linear regression line of RIN numbers for pH. Plot shows the effect of pH on RIN number for RNA samples isolated from 13 region of control brain tissue. No significant correlation was obtained with r-value = 0.0016 and p-value = 0.82. Samples with low pH value of < 5.9 were excluded.

Bar chart to show variation in %P by brain region (CRBL, WHMT).This graph shows the different performance of samples from specific brain regions on the array. These results are highly significant p-values (1.3 × 10−24 ). The heights of the bars represent the mean. The error bars represent the SEM.

Scatter plot for total RNA samples with linear regression line of Present call (%P) for pH. Scatter plot shows that pH significantly explains 12.0% of the variation in %P (p = 2.3 × 10−9, r = 0.353), including samples with low pH values. Low pH values are driving the regression analysis.

QuantiGene validation of microarray expression data. (a) SCN8A expression level between different regions. The graph shows high expression in OCTX compare with other regions. It is clear that this gene in mostly not expressed in WHMT region (expression level close to zero) also it presenting large error bar. (b) MAPT, showing higher expression in OCTX compare with other brain regions. These results confirm the array data with significant p-values of < 0.01. The expression level is presenting the mean and the error bars is SEM.

QuantiGene validation of microarray expression data for LRRK2 expression level in different regions. The graph shows higher expression in OCTX compare with other regions. Wilcoxon-signed rank test was performed and these results confirm the difference between regions in array data is significant. The expression level is presenting the median and the stars indicating the significant difference in expression with p-values of < 0.01. In this case, as LRRK2 expression level was very low, it was unreliable to use SEM and Wilcoxon’s test was performed using the median values.