Supplementary Tables 1 - 15 from Whole Transcriptome Sequencing Reveals Extensive Unspliced mRNA in Metastatic Castration-Resistant Prostate Cancer

Supplementary Table 1. Normalized RPKM expression values and normalized Affymetrix microarray intensity values for each CRPC sample used for correlation analysis. Supplementary Table 2. Complete listing of high probability, protein-coding somatic mutations detected by RNA-seq in CRPC samples. Mutations are classified as either a nonsense or missense single nucleotide variant (SNV) or as a >1 base insertion (INS) or deletion (DEL). The gene symbol and Genbank ID is provided for each predicted amino acid change given. Supplementary Table 3. High confidence putative fusions detected by ChimeraScan (at least one breakpoint-spanning read) and deFuse (greater than 50% probability score) for each CRPC sample. Supplementary Table 4. RPKM values for approximately 45,500 transcripts for all 8 CRPC samples. Supplementary Table 5. Top 100 expressed genes as measured by the mean RPKM across all 8 CRPC samples. Supplementary Table 6. Top 100 expressed genes as measured by the median RPKM across all 8 CRPC samples. Supplementary Table 7. Novel candidate lncRNAs observed CRPC. List is sorted by average FPKM for expression of the lncRNA. Supplementary Table 8. Transcripts, gene names, and gene description for the 1,465 transcripts with the widest range of expression used for unsupervised clustering of TCGA and CRPC samples. The average RPKM difference between CRPC and TCGA primary prostate cancers is shown. Supplementary Table 9. RNA-SeQC mapping statistics for 8 CRPC RNA-seq samples. For each sample, the Illumina instrument model, RIN score, type of run, and the number of total and uniquely-mapping reads is shown. In addition, it is indicated which percentage of quality-filtered reads mapped to exon, intron or intergenic coordinates, the number of Ensembl genes determined as expressed, and the percentage of reads mapping to ribosomal RNA. Supplementary Tables 10-11. Intronic RPB values for genes in CRPC 49 and 66. Supplementary Table 12. Global analysis of splicing in CRPC. For each CRPC sample, the number of sequence reads uniquely mapping to an exon-exon splice junction or overlapping an exon-intron splice boundary is shown. The percentage of unspliced out of the total is indicated. Supplementary Table 13. Primer sequences for the detection of correctly or incorrectly spliced portions of AR, KLK2, KLK3, STEAP2, CPSF6, and CDK19. Supplementary Table 14. Complete results for ChimeraScan on CRPC samples. Supplementary Table 15. Complete results for deFuse on CRPC samples.