Fig. 1

Mapping and coverage information. (a) The percentage of reads mapped to exons and to introns/intergenic regions out of the total number of uniquely mapped reads per sample. Color-code: purple for mRNA-seq protocol, orange for RiboZero protocol and blue for NuGEN ovation protocol. Black: FF samples (T1-T3), gray: ~ 4 years old FFPE samples (T1-T3), and light gray: ~ 10 years old FFPE samples (T4-T6, done only with mRNA-seq protocol). The amount of starting material, in ng, is indicated below the bars corresponding to each sample. (b) Box-plot of the percentages of reads uniquely mapped to exons out of total number of reads, for each sample type (FF mRNA-seq (T1-T3; n = 6); ~ 4 years old FFPE mRNA-seq (T1-T3; n = 5); ~ 10 years old FFPE mRNA-seq (T4-T6; n = 3); FF RiboZero (T1-T3; n = 3); FFPE RiboZero (T1-T3; n = 3); FFPE NuGEN ovation (T1-T3; n = 6)). n = number of measurements (#of tumor samples x number of initial RNA amounts). (c) The estimated number of detected genes as a function of the total number of reads for each sample type (FF mRNA-seq samples: purple solid line; FFPE mRNA-seq samples: purple dashed line, shown separately for ~ 4 and ~ 10 years old samples; FFPE RiboZero samples: orange dashed line). The horizontal dashed line represents the estimated coverage required for each sample type to get ~ 11,000 genes (see the numbers at the bottom (15 M, etc) for the estimated number of reads required for each sample type, and see methods for more details). (d) The average coverage along the relative genomic region from the 5′ end (Transcription Start Site) to the 3′ end (Transcription End Site) for each sample. mRNA-seq protocol at the left (purple; solid line for FF samples (T1-T3) and dashed line for FFPE samples (T1-T6)). RiboZero protocol to the right (orange; solid line for FF samples (T1-T3) and dashed line for FFPE samples (T1-T3))