DOI: 10.17026/dans-z6g-75da
title: Data from: Interacting Effects of Cell Size and Temperature on Gene Expression, Growth, Development and Swimming Performance in Larval Zebrafish

description: This dataset contains raw data of DNA content, gene expression levels, growth, development and swimming performanceof 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:- FCM_data.csvColumns:sample: file name of the FCM sampleploidy: ploidy level of the larvart: rearing temperature in degrees Celciuscycle: round of larval rearingstdpeak: annotated standard peak (internal standardisation with 2n peak of diploid larva)ratio: ratio of fluorescence peak of interest/peak Astdsize: genome size of zebrafish in picogramspg: weight in picograms of the peak of interestrcs: residual chi-square value, a goodness-of-fit value for the fitted modelphase: cell cycle phase of the peakfluor: fluorescence of the peak (no unit)count: number of nuclei in the peakperc: percentage of nuclei in this cell cycle phaseg2g1: ratio of cells in G2 phase compared to G1 calculated as G2/G1*100- Cell_phase_analysis.RR script for analysing densities of G1-phase cells and G2/G1 ratios- Gene_expr1.csvExpression of 6 housekeeping genes normalized for a combined index of the 5 other genesColumns:sample: number of sample; each sample contained 3 larvaeploidy: ploidy level of larvaert: rearing temperature in degrees Celciusgene: abbreviated gene nameexpr: relative quantitycq: cycle threshold value- Gene_expression_analysis.RR script for analysing gene expression data- Gene_expr2.csvExpression of metabolic genes normalized for rps11 and actb1Columns:sample: number of sample; each sample contained 3 larvaeploidy: ploidy level of larvaert: rearing temperature in degrees Celciusgene: abbreviated gene nameexpr: relative quantitycq: cycle threshold value- Gene_expression_analysis2.RR script for analysing gene expression data- Gene_exp3.csvExpression of metabolic genes normalized for all 6 housekeeping genesColumns:sample: number of sample; each sample contained 3 larvaeploidy: ploidy level of larvaert: rearing temperature in degrees Celciusgene: abbreviated gene nameexpr: relative quantitycq: cycle threshold value- Gene_expression_analysis3.RR script for analysing gene expression data- Development_larvae.csvColumns:cycle: round of larval rearingid: individual annotation of larvaploidy: ploidy level of larvart: rearing temperature in degrees Celsiushpf: hours post fertilizationdevst: developmental stagedevh: corresponding developmental hours- Development_analysis.RR script for analysing development data- DV_masterfile_allT.csvColumns: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- DV_analysis.RR script for analysing DanioVision data- Length_analysis.RR script for analysing length data- Materials and Methods.docxMaterials and methods section of the paper