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tktd_nrf2_zfe__data
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Dataset for the TKTD Nrf2 ZFE project

Ramo (Branch): main
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tktd_nrf2_zf...
Florian Schunck 27ce627c43 Changes to author list in ref publication 1 settimana fa
.datalad f81ca9d350 [DATALAD] new dataset 1 mese fa
.gitattributes 186bb2e278 Instruct annex to add text files to Git 1 mese fa
LICENSE c8b622d4a8 Change LICENSE 1 settimana fa
README.md 0983d3d9f3 Improve README formatting 3 settimane fa
datacite.yml 27ce627c43 Changes to author list in ref publication 1 settimana fa
dataset.csv bbc79c9c29 Add the dataset as csv file 3 settimane fa
tox.db 7a7b9fd41d Add tox.db database 1 mese fa

README.md

Survival, nrf2, internal concentration, and external concentration timeseries of zebrafish embryos exposed to Diuron, Diclofenac or Naproxen used in TKTD modelling

The dataset contains a number of experiments generated during 2015--2022 at the UFZ in Leipzig.

The data describe observations of different endpoints measured in zebrafish embryos (ZFE), exposed to the chemicals Diuron, Diclofenac and Naproxen (separately).

The observed endpoints were external concentrations, internal body residues in the ZFE, gene expression of nrf2 (a transcription factor that handles the stress response), and survival.

Usage

The recommended way to work with this dataset is with the companion code, available under https://github.com/flo-schu/tktd_nrf2_zfe/.

Data description

  • id: running number of the observation ID
  • treatment_id: ID that collects all measurements that were associated with the same chemical treatment (substance/concentration) with multiple replicates and repeated observations over time
  • experiment_id: ID of the experiments in which multiple treatments were conducted
  • nzfe: The number of zebrafish embryos (ZFE) used in 1 replicate of a given treatment
  • hpf: Hours post fertilization. The time of the exposure in h after the fertilization of the ZFE
  • substance: The chemical the ZFE was exposed to
  • cext_nom: The nominal concentration of the chemical in µmol/L
  • time: Time in hours (h) after the fertilization of the ZFE
  • cext: The concentration measured in the external medium
  • cint: The internal concentration, measured by homogenizing the ZFE
  • nrf2: The fold-change of the nrf2 expression level, relative to unexposed ZFE
  • lethality: The cumulative deaths observed in ZFE (number of ZFE dead at time t)

datafiles

  • tox.db: Contains the entire dataset including experiments and treatments that were not used in the final modeling dataset
  • dataset.csv: Includes only the data that was used for modeling
datacite.yml
Title Survival, nrf2, internal concentration, and external concentration timeseries of zebrafish embryos exposed to Diuron, Diclofenac or Naproxen used in TKTD modelling
Authors Kodritsch,Bernhard;Helmholtz-Centre for Environmental Research GmbH---UFZ, Permoserstr. 15, 04318 Leipzig, Germany
Schunck,Florian;Osnabrück University, Barbarastr. 12, 49076 Osnabrück, Germany;ORCID:0000-0001-7245-953X
Krauss,Martin;Helmholtz-Centre for Environmental Research GmbH---UFZ, Permoserstr. 15, 04318 Leipzig, Germany;ORCID:0000-0002-0362-4244
Focks,Andreas;Osnabrück University, Barbarastr. 12, 49076 Osnabrück, Germany;ORCID:0000-0002-9031-0808
Busch,Wibke;Helmholtz-Centre for Environmental Research GmbH---UFZ, Permoserstr. 15, 04318 Leipzig, Germany;ORCID:0000-0002-5497-6266
Description The dataset contains a number of experiments generated during 2015--2022 at the Helmholtz Centre for Environmental Research---UFZ in Leipzig. The data describe observations of different endpoints measured in zebrafish embryos (ZFE), exposed to the chemicals Diuron, Diclofenac and Naproxen (separately). The observed endpoints were external concentrations, internal body residues in the ZFE, gene expression of *nrf2* (a transcription factor that handles the stress response), and survival. The recommended way to work with this dataset is with the companion code, available under https://github.com/flo-schu/tktd_nrf2_zfe/.
License Creative Commons Attribution-ShareAlike 4.0 (https://creativecommons.org/licenses/by-sa/4.0/deed.en)
References Schunck F, Kodritsch B, Busch W, Kraus M, Focks A (2024) [doi:tba] (IsSupplementTo)
Analysis of scattered timeseries data from multiple experiments with pymob. Schunck 2024. Github [url:https://github.com/flo-schu/tktd_nrf2_zfe] (IsReferencedBy)
Funding
Keywords TKTD modelling
zebrafish
nrf2
internal concentration
gene expression
timeseries
survival
modelling
Resource Type Dataset