This dataset contains raw data of DNA content, gene expression levels, growth, development and swimming performance
of diploid and triploid larval zebrafish, used for analyses and figures of the Frontiers paper: Interacting effects of cell size and temperature on gene expression, growth, development and swimming performance in larval zebrafish by van de Pol, Hermaniuk and Verberk. In this paper we investigated the effects of cell size on gene expression, growth, development and swimming performance in zebrafish larvae at different temperatures. Details about the experimental procedures can be found in the Materials and Methods section of the paper. We have also included the R scripts for data analyses in this dataset. A brief description of the data files and column descriptions can be found below.
The datafiles include:
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FCM_data.csv
Columns:
sample: file name of the FCM sample
ploidy: ploidy level of the larva
rt: rearing temperature in degrees Celcius
cycle: round of larval rearing
stdpeak: annotated standard peak (internal standardisation with 2n peak of diploid larva)
ratio: ratio of fluorescence peak of interest/peak A
stdsize: genome size of zebrafish in picograms
pg: weight in picograms of the peak of interest
rcs: residual chi-square value, a goodness-of-fit value for the fitted model
phase: cell cycle phase of the peak
fluor: fluorescence of the peak (no unit)
count: number of nuclei in the peak
perc: percentage of nuclei in this cell cycle phase
g2g1: ratio of cells in G2 phase compared to G1 calculated as G2/G1*100
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Cell_phase_analysis.R
R script for analysing densities of G1-phase cells and G2/G1 ratios
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Gene_expr1.csv
Expression of 6 housekeeping genes normalized for a combined index of the 5 other genes
Columns:
sample: number of sample; each sample contained 3 larvae
ploidy: ploidy level of larvae
rt: rearing temperature in degrees Celcius
gene: abbreviated gene name
expr: relative quantity
cq: cycle threshold value
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Gene_expression_analysis.R
R script for analysing gene expression data
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Gene_expr2.csv
Expression of metabolic genes normalized for rps11 and actb1
Columns:
sample: number of sample; each sample contained 3 larvae
ploidy: ploidy level of larvae
rt: rearing temperature in degrees Celcius
gene: abbreviated gene name
expr: relative quantity
cq: cycle threshold value
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Gene_expression_analysis2.R
R script for analysing gene expression data
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Gene_exp3.csv
Expression of metabolic genes normalized for all 6 housekeeping genes
Columns:
sample: number of sample; each sample contained 3 larvae
ploidy: ploidy level of larvae
rt: rearing temperature in degrees Celcius
gene: abbreviated gene name
expr: relative quantity
cq: cycle threshold value
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Gene_expression_analysis3.R
R script for analysing gene expression data
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Development_larvae.csv
Columns:
cycle: round of larval rearing
id: individual annotation of larva
ploidy: ploidy level of larva
rt: rearing temperature in degrees Celsius
hpf: hours post fertilization
devst: developmental stage
devh: corresponding developmental hours
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Development_analysis.R
R script for analysing development data
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DV_masterfile_allT.csv
Columns:
rtemp: rearing temperature in degrees Celsius.
mtemp: measuring temperature in degrees Celsius.
individual: individual identifier.
trial: swimming performance trial.
rankstim: rank number of startle.
speed: velocity measured in mm/s. note that for startle = 0, this represents the average spontaneous velocity over 19 seconds after the startle stimulus.
lgspeed: 10 log of speed.
startle: startle = 1 means a startle stimulus was presented. startle stimulus = 0 means there was no startle stimulus, representing inter-startle-interval.
cs: cs = 1 means this larva received a cold shock to induce triploidy. cs = 0 means no cold shock was applied.
ploidy: ploidy level of larva.
responder: responder = 1 is defined as a larva that at least once showed a velocity higher than 15 mm/s. responder = 0 if a larva never showed a velocity higher than 15 mm/s.
length: length of larva in mm
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DV_analysis.R
R script for analysing DanioVision data
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Length_analysis.R
R script for analysing length data
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Materials and Methods.docx
Materials and methods section of the paper