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Datasets from "Optimal growth conditions of the haptophyte Chrysochromulina leadbeateri causing massive fish mortality in Northern Norway"

Clone repository (UNIX-like systems and macOS)

git clone https://github.com/Mr-Mathias-F/Chrysochromulina-leadbeateri-growth-rates

Experimental design

The study used a high-throughput experimental design to screen the growth rates of the fish-killing haptophyte Chrysochromulina leadbeateri, which caused massive fish mortality in Northern Norway in 1991 and 2019. The figure below shows a schematic depiction of the experimental design.

Fig_2

Data analysis

All files used for data processing, analysis and Arduino light panel programming are in the Analysis folder using R (version 4.2.1).

Fig_5

Datasets used in high-throughput Chrysochromulina leadbeateri (HTCL) growth rate experiments

HTCL_dataset_metadata.csv / HTCL_dataset_metadata.xlsx

Dataset with Chrysochromulina leadbeateri chlorophyll-a measurement with full metadata.

Column description:

  • Date_Time – Date (in YYYY-MM-DD format) and time (in HH:MM:SS format) for each in vivo chlorophyll-a measurement
  • Date – Date (in YYYY-MM-DD format) for each in vivo chlorophyll-a measurement
  • Time – Time (in HHMM format) for each in vivo chlorophyll-a measurement
  • Experiment.x – Experimental name
  • ID_unique – Unique well identifier for each plate (concatenation of well ID (Row and Col) with Plate.x)
  • Plate.x – Plate number in the experiment
  • ID – Well identifier
  • Row – Well row
  • Col – Well column
  • Chl – Measured in vivo chlorophyll-a measurement in Chrysochromulina leadbeateri
  • Well – Well identifier (identical to ID)
  • Plate.y – Plate number in the experiment (identical to Plate.x)
  • Light_panel – Identification of which light panel used
  • Group – Taxonomic clade of species
  • Genus – Taxonomic genus of species
  • Species – Taxonomic species name
  • Strain_Experiment_Replicate – Description of strain from which experiment and replicate (concatenation of Strain, Experiment.x and replicate)
  • Strain_Experiment – Description of strain from which experiment (concatenation of Strain and Experiment.x)
  • Strain – Strain of Chrysochromulina leadbeateri used
  • Species_Strain – Description of species and which strain (concatenation of Species and Strain)
  • Medium – Medium used in the experiment
  • Replicate – Identification of technical replicate within experiment for combination of culture condition
  • Salinity – Salinity treatment of the medium
  • Temperature – Temperature treatment (°C)
  • Light_period – Number of hours (h) with light on in a given day
  • Light_intensity – Irradiance treatment (µmol m-2 s-1)
  • Experiment.y – Identification of experiment
  • Timepassed – Time passed since starting experiment (based on the time of the first measurement)
  • Day – Time passed in number of days (rounded from Timepassed to integer)

metaPR2_Chrysochromulina_leadbeateri.csv / metaPR2_Chrysochromulina_leadbeateri.xlsx

Extracted data from the metaPR2 dataset for species Chrysochromulina leadbeateri.

Column description:

  • depth – Depth level (m) of the metabarcode sample
  • salinity – Salinity at sampling site
  • temperature – Temperature (°C) at sampling site
  • asv_code – Assigned amplicon sequence variant (ASV) code of Chrysochromulina leadbeateri
  • n_reads_pct – Percentage (%) read of ASV out of total reads
  • longitude – Coordinate indicating the north-south position of the sample (°N / °S)
  • latitude – Coordinate indicating the east-west position of the sample (°E / °W)

HTCL_dataset_validation.csv / HTCL_dataset_validation.xlsx

Dataset with Chrysochromulina leadbeateri strain UIO394 in vivo chlorophyll-a measurements and cell concentations (cells mL-1).

Column description:

  • Replicate – Identification of replicate
  • Day – Time passed (d) since experiment start
  • IVF_mean – Mean in vivo chlorophyll-a measurements of Chrysochromulina leadbeateri
  • IVF_sd – Standard deviation of mean in vivo chlorophyll-a measurements for technical replicates
  • Cell_conc – Cell concentration of Chrysochromulina leadbeateri determined by manual cell counting (cells mL-1)
  • Species – Taxonomic Species name
  • Temp – Temperature (°C)
  • Salintiy – Salinity of the medium
  • Date – Date (in DD-MM-YYYY format)

HTCL_mumax.xlsx

Dataset with Chrysochromulina leadbeateri maximum specific growth rates obtained from the spline models.

Column description:

  • Strain – Strain of Chrysochromulina leadbeateri used
  • Salinity – Salinity treatment of the medium
  • Temperature – Temperature treatment (°C)
  • Irradiance – Irradiance treatment (µmol m-2 s-1)
  • Experiment ID – Identification of experiment
  • Maximum specific growth rate – The maximum specific growth rate (d-1) estimated for given combination of Strain, Salinity, Temperature, Irradiance and Experiment ID
  • Standard deviation – Standard deviation of the maximum specific growth rates of all technical replicates for given combination of Strain, Salinity, Temperature, Irradiance and Experiment ID