File 1: name: neofl_CV_2015-TSAGHLB00000000 Annotation of Neocalanus flemingeri CV reference transcriptome used for the gene expression analysis. The TSA is available through National Center of Biotechnology Information (NCBI; BioProject: PRJNA496596, TSA: GHLB00000000). The transcriptome was annotated against SwissProt (downloaded 2015, e-value >10-6), Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. For each transcript, sequence ID, NCBI accession number, SwissProtEntryName, SwissProt e-value, annotation, EC number Cross-reference (KEGG), Gene ontology (GO) term and Gene ontology IDs are provided. File 2: name: nflem_3yearsPWS_edgeR-TMM-RPKM_kallisto_NCBI-acc Relative expression levels for Neocalanus flemingeri CV collected from Prince William Sound (two stations: PWS2, PWSA) during 2015(n=6),2016 (n=6) and 2017(n=10). Each sample was mapped against the reference transcriptome using kallisto. Counts were normalized using the RPKM (reads per kilobase of transcript length per million reads) method. File 3: name:DE_GLMtest(P<0.05-FDR) List of differentially expressed genes (DEGs)in Neocalanus flemingeri CVs collected from Prince William Sound (PWS)during 2015, 2016 and 2017. A generalized linear model (GLM) was used to identify differential gene expression across years using p-value <0.05 adjusted for false discovery rate (Benjamini-Hochberg correction). File 4: name:DE_Likelihoodtest_2015vs2016(P<0.05-FDR) List of differentially expressed genes (DEGs)in Neocalanus flemingeri CVs collected from Prince William Sound (PWS)during 2015 and 2016. DEGs were identified using the generalized linear model (GLM) followed by pairwise likelihood test between the two years (p-value <0.05 adjusted for False discovery rate (FDR)). File 5: name:DE_Likelihoodtest_2015vs2017(P<0.05-FDR) List of differentially expressed genes (DEGs)in Neocalanus flemingeri CVs collected from Prince William Sound (PWS)during 2015 and 2017. DEGs were identified using the generalized linear model (GLM) followed by pairwise likelihood test between the two years (p-value <0.05 adjusted for False discovery rate (FDR)). File 6: name: File7-DE_Likelihoodtest_2016vs2017(P<0.05-FDR) List of differentially expressed genes (DEGs)in Neocalanus flemingeri CVs collected from Prince William Sound (PWS)during 2016 and 2017. DEGs were identified using the generalized linear model (GLM) followed by pairwise likelihood test between the two years (p-value <0.05 adjusted for False discovery rate (FDR)). File 7: name: Glycolysis genes-Figure 4 List of differentially expressed genes involved in the glycolysis pathway in Neocalanus flemingeri CVs collected from Prince William Sound during 2015, 2016 and 2017 (Figure 4 in manuscript). Transcripts have been selected based on their annotation (EC number) and they are ordered by EC number as shown in Figure 4. Each EC number might include several transcripts that were annotated to the same protein. For each transcript, sequence ID, SwissProt e-value, annotation, EC number Cross-reference (KEGG) are provided. File 8: name:Glycolysis incoming pathway genes-Figure 5 List of differentially expressed genes involved in the glycolysis incoming pathways in Neocalanus flemingeri CVs collected from Prince William Sound during 2015, 2016 and 2017(Figure 5 in manuscript). Transcripts have been selected based on their annotation (EC number) and they are ordered by EC number as shown in Figure 5. Each EC number might include several transcripts that were annotated to the same protein. For each transcript, sequence ID, SwissProt e-value, annotation, EC number Cross-reference (KEGG) are provided. The file includes also transcripts annotated to EC involved in the glycolysis incoming pathways that were not among the differentially expressed genes (bold). Those transcripts (NO DEGs) were not included in Figure 5. File 9: name:TCA cycle genes-Figure 6 List of differentially expressed genes involved in the TCA cycle in Neocalanus flemingeri CVs collected from Prince William Sound during 2015, 2016 and 2017(Figure 6 in manuscript). Transcripts have been selected based on their annotation (EC number) and they are ordered by EC number as shown in Figure 6. Each EC number might include several transcripts that were annotated to the same protein. For each transcript, sequence ID, SwissProt e-value, annotation, EC number Cross-reference (KEGG) are provided. The file includes also transcripts annotated to EC involved in the TCA cycle that were not among the differentially expressed genes (bold). Those transcripts (NO DEGs) were not included in Figure 6. File 10: name: FA biosynthetic process genes-Figure 7 List of differentially expressed genes annotated with the GO term fatty acid biosynthetic process (GO:0006633) in Neocalanus flemingeri CVs collected from Prince William Sound during 2015, 2016 and 2017. Transcripts are ordered as shown in the heatmap in Figure 7. For each transcript, sequence ID, SwissProt e-value, annotation, EC number Cross-reference (KEGG), Gene ontology (GO)terms are provided. File 11: name: Cellular stress response, digestion and muscle contraction genes-Figure 8 List of differentially expressed genes annotated with the GO terms cellular response to stress (GO:0033554), digestion (GO:0007586) and muscle contraction (GO:0006936) in Neocalanus flemingeri CVs collected from Prince William Sound during 2015, 2016 and 2017. Transcripts are ordered as shown in the heatmap in Figure 8. For each transcript, sequence ID, SwissProt e-value, annotation, EC number Cross-reference (KEGG), Gene ontology (GO)terms are provided.