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Fig. 3 | BMC Genomics

Fig. 3

From: mRNA-seq whole transcriptome profiling of fresh frozen versus archived fixed tissues

Fig. 3

Comparison of fold-changes measured for FFPE samples versus matched FF samples. (a) Scatter plot for the expression fold changes (log2 scale) of ~ 23,000 genes measured in T1 vs. T2, obtained from FF samples (x-axis) compared to matched FFPE samples (y-axis) by mRNA-seq protocol (purple). R2 and correlation coefficient are presented at the plot. (b) Scatter plot for the expression fold changes (log2 scale) of ~ 23,000 genes measured in T1 vs. T2, obtained from FF samples (x-axis) compared to matched FFPE samples (y-axis) by RiboZero protocol (orange). R2 and correlation coefficient are presented at the plot. (c) For each comparison in (a)-(b) the percentages of differentiating genes by FFPE samples (2fold) that are in agreement or disagreement with the FC of matched FF samples are presented (see methods for more information). In addition, the same percentages are presented for the FC comparing T1 vs. T3 and T2 vs. T3 for the mRNA-seq protocol. Purple bars represent the mRNA-seq protocol and orange bar for RiboZero protocol. (d) Same as (c), presented for fold-change threshold values (imposed on the FFPE samples) varying between 1 to 10 (x-axis). The y-axis shows the percentage of differentiating genes in FFPE that changed in the same direction as in matched FF samples. Purple for mRNA-seq protocol and orange for RiboZero protocol

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