Fig. 2

Comparisons of matched FF and FFPE samples prepared with different RNA-seq protocols. (a) Scatter plot of gene expression levels as measured from FFPE sample T1 by mRNA-seq protocol (purple; left) and RiboZero protocol (orange; right), compared to the gene expression data obtained from the FF sample of the same tumor . Gene expression data presented in log2 scale; r-square and correlation coefficients are presented for each plot. Total number of reads for each library is indicated at the x and y labels (M = million) (b) Same as (a) for the T2 samples (c) Same as (a) for T3. (d) Pearson correlation coefficient matrix between T1 gene expression data as measured by the different protocols: mRNA-seq in purple, RiboZero in orange and NuGEN ovation in blue, on the FF (black) and FFPE (gray) samples (colorbar at the bottom), measured for the indicated RNA quantities (in ng). The colorbar to the right is for the correlation coefficient values from 0 to 1. (e) Same as (d) for T2 (f) Same as (d) for T3