Files in this data supplement:
- Supporting Information: Figures S1-S5, File S1, and Tables S1-S12 (PDF, 1 MB)
- Figure S1: Characterization of sequencing depth and unique read threshold on estimation of allele-specific expression. (PDF, 544 KB)
- Figure S2: Comparison of Chromosome 10 founder coefficient plots for Rps12-ps2 expression derived from alignment to NCBIM37 or individualized DO transcriptomes. (PDF, 446 KB)
- Figure S3: Comparison of gene-level expression in Founder strain samples and founder allele-level estimates in the DO samples for genes with and without significant local eQTL after alignment to individualized genomes. (PDF, 159 KB)
- Figure S4: Strain polymorphisms between NCBIM37 and CAST in Ftl1 and Ftl2 transcript sequences can bias alignment of CAST-derived Ftl1 reads. (PDF, 455 KB)
- Figure S5: Coverage of CAST reads to Ftl1 and Ftl2 transcript sequences derived from the NCBIM37 reference genome and individualized CAST genome. (PDF, 272 KB)
- File S1: Supplemental Methods (PDF, 142 KB)
- Table S1: Isoform-level summary of read alignment in the simulated CAST data. (PDF, 150 KB)
- Table S2: List of genes from the CAST simulation that were affected by read misalignment or alignment failure from the reference alignment strategy. (.zip, 637 KB)
- Table S3: Comparison of gene-level abundance results from alignment of 30 million simulated CAST reads to NCBIM37 and CAST transcriptomes. (PDF, 173 KB)
- Table S4: List of genes from the DO simulation that were affected by read misalignment or alignment failure from the reference alignment strategy. (.zip, 393 KB)
- Table S5: Comparison of gene-level abundance results from alignment of 30 million simulated DO reads to NCBIM37 and individualized DO transcriptomes. (PDF, 142 KB)
- Table S6: Alignment statistics for real CAST and DO liver RNA-seq data. (PDF, 188 KB)
- Table S7: eQTL simulation summary showing the classification of eQTL calls that differ between alignment strategies differentiated by gene biotype. (PDF, 149 KB)
- Table S8: Gene-level summary of eQTL simulation results. (.zip, 3 MB)
- Table S9: List of eQTL from alignment to individualized DO transcriptomes. (.zip, 603 KB)
- Table S10: List of eQTL from alignment to NCBIM37. (.zip, 627 KB)
- Table S11: Isoform abundance results in CAST simulation study. (PDF, 172 KB)
- Table S12: Comparison of isoform abundance results in CAST simulation study from using paired-end or single-end sequencing. (PDF, 144 KB)