Additional file 1 of Loci associated with variation in gene expression and growth in juvenile salmon are influenced by the presence of a growth hormone transgene

Additional file 1: Table S1. Genes differentially expressed between large transgenic (TLarge) and non-transgenic (NTLarge) fish with a ≥ 3 fold change in expression level. Negative log2Ratios indicate genes that had higher expression levels in NTLarge while positive values are genes with higher expression levels in TLarge. Table S2. Genes differentially expressed between small transgenic (TSmall) and non-transgenic (NTSmall) fish with a ≥ 3 fold change in expression level. Negative log2Ratios indicate genes that had higher expression levels in NTSmall while positive values are genes with higher expression levels in TSmall. Table S3. Genes differentially expressed between large (TLarge) and small (TSmall) transgenic (T) fish with a ≥ 3 fold change in expression level. Negative log2Ratios indicate genes that had higher expression levels in TLarge while positive values are genes with higher expression levels in TSmall. Table S4. Genes differentially expressed between large (NTLarge) and small non-transgenic (NTSmall) fish with a ≥ 3 fold change in expression level. Negative log2Ratios indicate genes that had higher expression levels in NTLarge while positive values are genes with higher expression levels in NTSmall. Table S5. Gene Ontology (GO) Biological Process categories for differentially expressed genes (DEGs) identified in comparisons between transgenotypes within size groups (large non-transgenic, NTLarge; large transgenic, TLarge; small non-transgenic, NTSmall; and small transgenic, TSmall). The total number of DEGs found in GO categories in the whole genome are given as well as observed (obs) and expected (exp) GO terms represented in the study dataset. The c2 value for GO terms where the observed number of DEGs differed significantly from expected (p < 0.05) is given (c2), along with deviations (dev) from expected as observed - expected, and the relative percent (rel %) of the genome represented by that GO-term. Table S6. Gene Ontology (GO) Biological Process categories for the differentially expressed genes identified in comparisons between size groups within transgenotypes (large non-transgenic, NTLarge; large transgenic, TLarge; small non-transgenic, NTSmall; and small transgenic, TSmall). The total number of DEGs found in GO categories in the whole genome are given as well as observed (obs) and expected (exp) GO terms represented in the study dataset. The c2 value for GO terms where the observed number of DEGs differed significantly from expected (p < 0.05) is given (c2), along with deviations (dev) from expected as observed - expected, and the relative percent (rel %) of the genome represented by that GO-term. Table S7. SNP markers that were significantly associated with expression levels of assessed genes or phenotypic traits in different size groups of either Transgenic (T) or Non-Transgenic (NT) fish. P-values from the GLM analysis are given along with the adjusted q value (FDR = 0.05); significant q values are shown in bold. Traits are as for Table 1; linkage groups (LG) with NCBI Reference numbers (REF), and position (POS) on the linkage group are given, along with the Major and Minor alleles for each SNP. a: SNP marker associated with multiple traits; b: the same marker associated with different traits in T and NT; c: the same marker associated with different traits between size classes. Table S8. The number of transgenic and non-transgenic coho salmon with their mean (standard deviation) weight, length and condition factor (CF) at the time of sampling. Table S9. Gene names and products for traits analysed by qPCR and Open Array. Oligo sequences of forward (F) and reverse (R) primers and probes are given along with gene locations and NCBI transcriptome IDs (for Open Array genes). General functions are indicated.