Data from: Exposure to warmer water and prenatal cortisol independently alter transcriptional plasticity during early development in Chinook salmon (Oncorhynchus tshawytscha)
Data files
Jan 26, 2026 version files 1.90 MB
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DeltaCT_EF-1A_Endogenous_Control_Corrected_PCR_Efficiency.csv
1.03 MB
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Eyed_BoxCox_dCq.csv
41.34 KB
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README.md
4.73 KB
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Survival_Binary_Alevin.csv
265.68 KB
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Survival_Binary_Eyed.csv
319.70 KB
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Survival_Binary_Fry.csv
237.92 KB
Abstract
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).
title: "README"
author: "C Finerty"
date: "2025-12-04"
output: html_document
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
