New Levels of Transcriptome Complexity at Upper Thermal Limits in Wild Drosophila Revealed by Exon Expression Analysis

Supporting Information

Supporting Information

Supporting Information - Figures S1-S6, File S1, and Tables S1-S12 (PDF, 1 MB)
Figure S1 - High signal comparability of the 3'IVT (black line) and exon modules (grey line) for eight thermally responsive Hsps. (PDF, 445 KB)
Figure S2 - Average linkage hierarchical clustering of the eight point time-series across three replicates for the significant time-point term (FDR 0.2). (PDF, 419 KB)
Figure S3 - Short time-series expression miner (STEM) profiles of 1078 genes identified from the 3'IVT probe module with ANOVA. (PDF, 471 KB)
Figure S4 - Up-regulation of genes spanning the repertoire of Drosophila innate immune response (PDF, 451 KB)
Figure S5 - Detailed transcript analyses of early responding genes confirm RNA splicing inhibition during heat shock. (PDF, 488 KB)
Figure S6 - Raw data for PCR data for multi-transcript genes using exon-junction primers to target mature mRNA levels and intron/exon primers to target pre-mRNA levels relative to RpL11 (Y-axis). (PDF, 451 KB)
File S1 - Supplementary results (PDF, 314 KB)
Table S1 - Primer sequences for real-time PCR (PDF, 439 KB)
Table S2 - Kappa statistics for signal intensity agreement within modules at the individual (raw) probe, normalized probeset, and gene levels. (PDF, 433 KB)
Table S7 - Results for two-way ANOVAs testing for expression changes over time following heat stress (time term), transcript-type (transcript, mRNA or pre-mRNA) and interaction term. (PDF, 437 KB)
Table S8 - Results for one-way ANOVAs with Dunnett's tests comparing pre-stress relative transcript abundances with high temperature (38.5°) and recovery (25C°). (PDF, 454 KB)
Table S9 - ANOVA results for model III fit with the constitutive exons as a covariate for 1,094 genes with constitutive exons and at least two alternative exons (PDF, 430 KB)
Table S3 - Gene level average log background corrected signals from Model I analyses (fixed term of time-point). (.xlsb, 10 MB)
Table S4 - STEM profiling for significant genes (time-point term) from the constitutive exon analysis. (.xlsx, 85 KB)
Table S5 - DAVID functional annotation clustering analysis of the genes from the enriched recovery STEM profiles as well as the 'early up' profiles from the gene-level analyses (FDR 0.05). (.xlsx, 81 KB)
Table S6 - Table of genes spanning the repertoire of the Drosophila innate immune response from the gene-level (constitutive probeset) analyses. (.xlsx, 22 KB)
Table S10 - Isoform/isoform subset level average log background corrected signals from Model II and III analyses (.xlsx, 19 MB)
Table S11 - STEM profiling for significant multi-transcript genes from the master list (time-point term, time-point-by-exon-type interactions). (.xlsx, 69 KB)
Table S12 - DAVID functional annotation clustering analysis of the isoforms/subsets from the enriched recovery STEM profiles as well as the 'early up' profiles from the significant genes from the master list from models II and III (.xlsx, 69 KB)