This file explains all of the variables in each of the datasets that accompany: Toews, SD, Wellband, KW, Dixon, B, & Heath, DD. (2018). Variation in juvenile Chinook salmon (Oncorhynchus tshawytscha) transcription profiles among and within eight population crosses from British Columbia, Canada Source Populations: BQ = Big Qualicum River CAP = Capilano River CHILL = Chilliwack River NIT = Nitinat River PUNT = Puntledge River QUIN = Quinsam River RC = Robertson Creek YIAL = Yellow Island Aquaculture Ltd. (domestic population) -------------- Gene Name Annotations: B-ACTIN = beta-actin CAL = calmodulin CK-1 = chemokine-1 COI = cytochrome oxidase 1 CPT1 = carnitine palmytol transferase 1 CYP1A = cytochrome p450 family 1A EF-1A = elongation factor 1A EGR-1 = early growth response protein 1 GH-R = growth hormone receptor GR2 = glucocorticoid receptor 2 HSP70 = heat shock protein 70 HSP90A = heat shock protein 90a IGF-1 = insulin-like growth factor 1 IGFBP2B = insulin-like growth factor binding protein 2b IL-1B = interleukin 1B IL-8 = interleukin 8 LEPTIN = leptin 1 META = metallothionein A MHCIIB = major histocompatibility complex class 2B MYO1A = myostatin 1A NKEF = natural killer enhancing factor P53 = tumor supressor protein p53 PEPCK = phosphoenolpyruvate carboxykinase PK = pyruvate kinase SAA = serum amyloid A THR-B = thyroid hormone receptor b TNF-A = tumor necrosis factor a -------------- General Definitions DCt = delta critical threshold (the Ct value normalized to the housekeeping gene) Log.DCt = log-transformed DCt (used in analyses) DDCt = delta delta critical threshold (the DCt value for a treated individual normalized to the average DCt for the control fish of the same family) Log.DDCt = log-transformed DDCt (used in analyses) -------------- Dataset Variables dataset: Toews_2018_Raw_qPCR_Data_Chinook_Transcription.txt Well = the well of the TaqMan OpenArray chip that the sample was loaded into Sample_Name = individual sample name Target_Name = the candidate gene Cq = the critical threshold value calculated by the QuantStudio 12K Flex dataset: Toews_2018_PCR_Efficiencies_Chinook_Transcription.txt Gene = the candidate gene PCR_Efficiency = the primer efficiency calculated in LinRegPCR and used in the calculation of DCt and DDCt dataset: Toews_2018_Processed_qPCR_Data_Chinook_Transcription.txt OpenArray_Chip = the chip the sample was loaded onto Treatment = the corresponding treatment for that individual, either: control, immune, or stress Tank = the replicate tank the individual resided in Sire = the sire and/or family i.d. (ex. P5 = Puntledge male number 5) Population = the source river population of the sires Weight = the weight of the individual at time of sampling Sample_Name = the name of the individual sample Target_Name = the candidate gene Cq_Mean = the average Cq (fractional cycle number) of the 2 technical replicates Nq = the arbitrary fluorescence threshold used in the calcaultion of DCt (was set to 1,000,000) E = primer efficiency Cshift = the c-shift, equal to: (log(1/(1-(1/E)))/log(E)) No = target quantity in arbitrary fluorescence units, equal to: Nq/(E^(Cq+Cshift)) EF1a = the corresponding No for the house-keeping gene (EF-1a) for that individual DCt = the corrected cycle number that was then log-transformed for analysis, calculated as: No/EF1a dataset: Toews_2018_Sample_Annotation_Chinook_Transcription.txt OpenArray_Chip = the chip the sample was loaded onto Treatment = the corresponding treatment for that individual, either: control, immune, or stress Tank = the replicate tank the individual resided in Sire = the sire and/or family i.d. (ex. P5 = Puntledge male number 5) Population = the source river population of the sires Weight = the weight of the individual at time of sampling Sample_Name = the name of the individual sample dataset: Toews_2018_R_Source_Code_Chinook_Transcription.txt The codes included in this file contain all of the codes run in R. This includes the treatment effect analysis, the population and sire effect analyses, the PCAs, all FDR corrections, and the Tukey test for NKEF. This file only contains a single replicate of each analysis, as each one was replicated per gene and/or per treatment (notes on this are included as comments in the file).