DOI: 10.5061/dryad.zgmsbccpm
title: Data from: Exposure to warmer water and prenatal cortisol independently alter transcriptional plasticity during early development in Chinook salmon (<em>Oncorhynchus tshawytscha</em>)

description: Freshwater ecosystems are changing rapidly from human induced rapid
 environmental change. Determining whether organisms have the adaptive
 capacity to respond to stressors and by which mechanisms remains a
 challenge. Within the Environmental-Match framework, we experimentally
 manipulated a maternal signal of environmental stress to see if it primed
 gene transcription plasticity to allow developing Chinook salmon
 (Oncorhynchus tshawytscha) to respond to water temperatures expected from
 climate modeling. Our OpenArray® chip approach across four functional
 groups (growth, metabolism, immune, stress) revealed that elevated
 temperatures induced a diversity of effects on gene transcriptional
 profiles at different early life stages for candidate genes at all levels
 of the hierarchical evaluation (complete gene sets, functional gene
 groups, individual gene transcriptional phenotypes). However, contrary to
 predictions, prenatal cortisol did not alter these transcriptional effects
 further and did not rescue temperature-driven increases in mortality.
 Results suggest that while exposure to signals of maternal stress have the
 capacity to induce complex life stage- and system-specific responses, they
 may not further mitigate existing responses induced by elevated water
 temperatures in Chinook salmon (possibly other species).
description: --- title: "README"\ author: "C Finerty"\ date:
 "2025-12-04"\ output: html_document --------------------- #
 **Exposure to warmer water and prenatal cortisol independently alter
 transcriptional plasticity during early development in Chinook salmon
 (*Oncorhynchus tshawytscha*)**: Open Source Data --- We have submitted our
 raw data
 (**DeltaCT_EF-1A_Endogenous_Control_Corrected_PCR_Efficiency.csv**),
 transformed data (**Eyed_BoxCox_dCq.csv**,**Fry_BoxCox_dCq.csv**),
 survival raw data
 (**Survival_Binary_Eyed.csv**,**Survival_Binary_Alevin.csv**,**Survival_Binary_Fry.csv**), and R markdowns of stagextemp interactions and survival (**Chapter 1 Stages (Cort x Temp)**,**Survival 2017-2018 (New)**) ## Descriptions ### **DeltaCT_EF-1A_Endogenous_Control_Corrected_PCR_Efficiency.csv**_Data * *Unique ID*: Sample Name + Target Gene * *Sample Name*: Name of sample comprised of maternal origin (female 1-8), cortisol treatment and replicate number (cortisol or non-cortisol; 2 replicates of each), and Heath cell replicate number (cell 1-3) * *Target Gene*: Genes evaluated for transcriptional variation * *Amplification Scores*: Metric of PCR efficiency and quality to identify reliable DNA quantification * *Cycle Quotient (Cq) Confidence*: Metric for flagging amplification curves of wells in Taqman Plate that perform poorly to be removed * *Cycle Threshold (CT)*: The minimum number of amplification cycles required for detection * *CT Mean*: The mean CT of the two replicates for each sample on the Taqman plate * *Efficiency*: Efficiency scores for amplification within the Taqman plate wells * *C Shift*: A correction factor applied in the analysis of qPCR data to account for an efficiency-dependent horizontal shift in the Cq value * *Nq*: Concentration of product at the quantification threshold * *N0*: Initial target quantity (starting concentration) * *EF-1A*: Endogenous control gene (EF-1A) Cq values corrected to control for Nq and N0 * *dCt*: Delta Ct corrected for by each samples endogenous gene (EF-1A) * *Female ID*: Females eggs used for fertilization * *Cortisol Treatment*: Solution treatment at fertilization containing dissolved cortisol or no cortisol * *Temperature Treatment*: Incubation temperatures following ambient conditions or predicted future ambient conditions * *Tray*: Incubation tray offspring were raised in in the Heath Stacks * *Cell*: Cells within each incubation tray (1-16) * *Developmental Stage*: Life history stage that samples were collected at for analysis (E = eyed-egg, A = alevin, F = button-up fry) ### Eyed_BoxCox_dCq.csv_Data * *Sample*: Name of sample comprised of maternal origin (female 1-8), cortisol treatment and replicate number (cortisol or non-cortisol; 2 replicates of each), and Heath cell replicate number (cell 1-3) * *Female ID*: Females eggs used for fertilization * *Replicate ID*: Replicate of each cortisol treatment (1-4) * *Cortisol Treatment*: Solution treatment at fertilization containing dissolved cortisol or no cortisol * *Temperature Treatment*: Incubation temperatures following ambient conditions or predicted future ambient conditions * *Cortisol x Temperature Treatment*: Cortisol Treatment + Temperature Treatment * *Tray*: Incubation tray offspring were raised in in the Heath Stacks * *Cell*: Cells within each incubation tray (1-16) * *Developmental Stage*: Life history stage that samples were collected at for analysis (E = eyed-egg, A = alevin, F = button-up fry) * *Cell Replicate*: Replicates of cell effects for fertilized eggs and cortisol treatments within the incubation stacks * *CAL-BC to TRXR3a-Log*: BoxCox transformed delta Ct values for genes of interest based on determined best normalcy in R * *Mass*: Mass of each sample ### **Survival_Binary_Eyed.csv**,**Survival_Binary_Alevin.csv**,**Survival_Binary_Fry.csv**_Data * *Tray ID*: Incubation tray offspring were raised in in the Heath Stacks * *Cell ID*: Cells within each incubation tray (1-16) * *Female*: Females eggs used for fertilization * *Temperature*: Temperature treatment (elevated vs current) * *Treatment*: Cortisol treatment at fertilization (cortisol vs non-cortisol) * *Treatment Replicate*: Replicate of each cortisol treatment (1-4) * *Cell Replicate*: Replicates of cell effects for fertilized eggs and cortisol treatments within the incubation stacks * *Stage*: Life history stage that samples were collected at for analysis (E = eyed-egg, A = alevin, F = button-up fry) * *Alive in Stage*: Number of individuals alive in the cell once developmental stage was achieved * *Dead*: Number of individuals deceased once developmental stage was achieved * *Percent Survival*: Percentage of survival at each developmental stage within the cell