Table 1.
Overview of FFPE cardiac tissue RNA extraction methods.
Fig 1.
Overview of experiment design.
Fig 2.
Assessment of RNA quality metrics in cardiac tissue FFPE derived RNA extract.
(A) Box and whisker plots (min to max) of RNA concentration and RNA purity assessment of 260/230 and A260/280 absorbance ratio based on absorption spectra in RNA samples extracted using Method QP versus Method QE (B) Box and whisker plots (min to max) of RNA concentration and RNA purity assessment of 260/230 and A260/280 absorbance ratio based on absorption spectra in RNA samples extracted using Method BL versus Method BP (C) Comparison across four methods of extraction, Box and whisker plots (min to max) of RNA concentration, RNA purity assessment of 260/230 and A260/280 absorbance ratio across method BL and BP vs Method QE and Method QP (D) Electrophoregram/RNA fragment length across the four methods. For all groups, the asterisk (*) denotes a significant difference between groups, Paired Wilcoxon Signed Rank Test (*p<0.05, ***p<0.005, ****p<0.001).
Table 2.
Comparison of RNA quality metrics across RNA extraction from FFPE cardiac tissue samples.
Fig 3.
Sequence data comparison between Method BL and Method QE.
(A) Correlation plot of normalized gene and transcript count. Data was normalized by log2(TPM+1). Each dot constitutes a gene or transcript. (B) Distribution of Exon, introns, and rRNA mapped reads (C) Heat map of top 25 genes and transcript across extracts from Method QE and Method BL.
Table 3.
Overview of sequencing characteristics across Method QE and Method BL.
Fig 4.
RT-qPCR analysis comparing Method QE and the optimized extraction method (Method BL).
(A) Box plots of individual Ct values for genes MYL2, MYH7, and MYH6 depict significant differences in gene expression detection. For all groups, an asterisk (*) denotes a significant difference between groups, Paired Wilcoxon Signed Rank Test (*p<0.05, ***p<0.005, ****p<0.001).
Table 4.
Summary of qPCR result.