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.

附加文件1：表S1。表达水平变化≥3倍的大型转基因鱼（TLarge）与非转基因大型鱼（NTLarge）之间的差异表达基因（differentially expressed genes, DEGs）。负log₂比值代表在NTLarge中表达更高的基因，正值则代表在TLarge中表达更高的基因。
附加文件1：表S2。表达水平变化≥3倍的小型转基因鱼（TSmall）与非转基因小型鱼（NTSmall）之间的差异表达基因。负log₂比值代表在NTSmall中表达更高的基因，正值则代表在TSmall中表达更高的基因。
附加文件1：表S3。表达水平变化≥3倍的大型转基因鱼（TLarge）与小型转基因鱼（TSmall）之间的差异表达基因。负log₂比值代表在TLarge中表达更高的基因，正值则代表在TSmall中表达更高的基因。
附加文件1：表S4。表达水平变化≥3倍的大型非转基因鱼（NTLarge）与小型非转基因鱼（NTSmall）之间的差异表达基因。负log₂比值代表在NTLarge中表达更高的基因，正值则代表在NTSmall中表达更高的基因。
附加文件1：表S5。针对同体型分组内不同转基因类型（大型非转基因鱼NTLarge、大型转基因鱼TLarge、小型非转基因鱼NTSmall、小型转基因鱼TSmall）间比较所鉴定出的差异表达基因的基因本体（Gene Ontology, GO）生物过程分类。本研究数据集中共统计了全基因组GO分类下的差异表达基因总数，以及观测到（obs）和预期（exp）的GO条目数。针对观测到的差异表达基因数与预期值存在显著差异（p<0.05）的GO条目，给出其卡方（c²）值、与预期值的偏差（dev，即观测值-预期值），以及该GO条目占基因组的相对百分比（rel %）。
附加文件1：表S6。针对同转基因类型内不同体型分组（大型非转基因鱼NTLarge、大型转基因鱼TLarge、小型非转基因鱼NTSmall、小型转基因鱼TSmall）间比较所鉴定出的差异表达基因的基因本体（GO）生物过程分类。本研究数据集中共统计了全基因组GO分类下的差异表达基因总数，以及观测到（obs）和预期（exp）的GO条目数。针对观测到的差异表达基因数与预期值存在显著差异（p<0.05）的GO条目，给出其卡方（c²）值、与预期值的偏差（dev，即观测值-预期值），以及该GO条目占基因组的相对百分比（rel %）。
附加文件1：表S7。在不同体型分组的转基因（T）或非转基因（NT）鱼中，与目标基因表达水平或表型性状显著相关的单核苷酸多态性（single nucleotide polymorphism, SNP）标记。本研究给出了广义线性模型（generalized linear model, GLM）分析得到的P值，以及校正后的q值（假发现率false discovery rate, FDR=0.05）；显著的q值以粗体标注。性状定义同表1；同时给出了连锁群（linkage group, LG）及其NCBI参考编号（REF）、该标记在连锁群上的位置（POS），以及每个SNP的主要等位基因和次要等位基因。注：a：与多个性状相关的SNP标记；b：在转基因与非转基因群体中与不同性状相关的同一标记；c：在不同体型分组间与不同性状相关的同一标记。
附加文件1：表S8。采样时的转基因与非转基因银大麻哈鱼数量，及其体重、体长和条件系数（condition factor, CF）的平均值（标准差）。
附加文件1：表S9。通过实时定量聚合酶链式反应（quantitative polymerase chain reaction, qPCR）和Open Array芯片分析的性状对应的基因名称及产物。本研究给出了正向（F）、反向（R）引物及探针的寡核苷酸序列，同时提供了基因位置以及Open Array相关基因的NCBI转录组编号。此外还标注了各基因的一般功能。