This dataset contains raw data of gene expression levels, cell size, cell number, growth, development and swimming performance of diploid and triploid larval zebrafish, used for analyses and figures of the PLOS ONE paper: Triploidy in zebrafish larvae: effects on gene expression, cell size and cell number, growth, development and swimming performance. (2020) by van de Pol, Flik and Verberk. In this paper we investigated the use of triploid zebrafish as a model to study cell size consequences. 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 data files include:

• Gene_expression_hkgenes.csv Columns: gene: abbreviated name of housekeeping gene. ploidy: ploidy level of larvae. sample: number of sample; each sample contained 3 larvae. dpf: days post fertilisation; indicates the sampling time. expr: relative quantity of housekeeping genes normalised for the other five housekeeping genes.

• qpcr_series.r R script for analysing gene expression data.

• cellnumber.csv Columns: ploidy: ploidy level of larva. cell number: cell number calculated as the sum of cells in G1, G2 and G3 (6n or 9n) phase. sample: sample number; these are paired data.

• cell_number_analysis.r R script for analysing cell numbers.

• ratioG2G1.csv Columns: ploidy: ploidy level of larva. ratioG2G1: calculated as G2/G1*100.

• ratio_g1g2.r R script for analysing G2/G1 ratios.

• Cell_size.csv Columns: ploidy: ploidy level area: cell area in μm2 vol: cell volume in μm3 code: factor 1 = 3n, factor 0 = 2n.

• cell_area.r R script for analysing cell area and cell volume.

• devstages26.5ref.csv Columns: cycle: refers to the week/batch in which the larvae were sampled. id: identifier number of larvae. ploidy: ploidy level of larva. rt: rearing temperature in degrees Celsius. hpf: hours post fertilisation; indicates the sampling time (as factor). devst: developmental stage in which the larvae were categorised. devh: corresponding hours post fertilisation. ref: "real" hours post fertilisation (as integer).

• development_data.r R script for analysing development rate.

• length.csv Columns: ind: individual identifier. batch: refers to the week/batch in which the larvae were sampled. rearT: rearing temperature in degrees Celsius. Length: length in mm. ploidy: ploidy level of larva.

• length_data.r R script for analysing length of diploid and triploid larval zebrafish.

• Swimming_performance.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.

• daniovision_data.r R script for analysing swimming performance.

• assessing_ploidy_levels.r R script for analyzing ploidy levels on .LMD files.

• description data files.docx A description of all before mentioned data files.

• Materials and methods.docx Materials and methods section of the paper: Triploidy in zebrafish larvae: effects on gene expression, cell size and cell number, growth, development and swimming performance. (2020) by van de Pol, Flik and Verberk.