Additional file 1 of Alternative splicing is highly variable among Daphnia pulex lineages in response to acute copper exposure

Additional file 1: Table S1. Quality and mapping information for the 21 Daphnia pulex RNA-sequencing libraries against both the JGI V1.0 2011 assembly from Ensembl (as reported in Table S3 in Chain et al. 2019 [53]) and also against the newer Daphnia PA42 3.0 reference assembly from Ye et al. 2017 [42]. Sample names consist of tank number (T), individual ID number, and clone (D, K or S). Samples were run in one of two lanes, and average quality (Q) is presented as PHRED scores. The % mapped reads and number of expressed genes are shown for each of the reference assemblies, as well as the alternative spliced genes against the newer reference. Table S2. Differentially expressed genes in response to acute Cu exposure when comparing all 6 controls with all 15 Cu exposed samples. Table S3. Summary of blast analysis comparing the differentially expressed (DE) genes identified by Chain et al. [53] with the genes from the newer Daphnia PA42 3.0 reference assembly from Ye et al. 2017 [42]. Table S4. Comparison of the DE genes identified by Chain et al. 2019 [53] and the genes from the newer Daphnia PA42 3.0 reference assembly from Ye et al. 2017 [42] using BLASTn. Table S5. Differentially spliced genes in response to acute Cu exposure when comparing all 6 controls with all 15 Cu exposed samples. Δ|Ψ| is the difference in the exon/intron inclusion level between the two conditions. Table S6. Differentially expressed genes in response to acute Cu exposure from clone specific analyses. Table S7. Genes commonly differentially expressed from global analysis and clone specific analyses. Table S8. Differentially spliced genes in response to acute Cu exposure in Clone D. Table S9. Differentially spliced genes in response to acute Cu exposure in Clone S. Table S10. Differentially spliced genes in response to acute Cu exposure in Clone K. Table S11. Gene Ontology enrichment analysis of the DE genes from the global analysis combining all 6 controls with all 15 Cu exposed samples (BP: biological process, MF: molecular function). Table S12. Gene Ontology enrichment analysis of the DE genes from clone specific analyses (BP: biological process, MF: molecular function). Table S13. Gene Ontology enrichment analysis of the DS genes from the global analysis combining all 6 controls with all 15 Cu exposed samples (BP: biological process, MF: molecular function). Table S14. Gene Ontology enrichment analysis of the DS genes from clone specific analyses (BP: biological process, MF: molecular function).