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Liu, Tzu-Yen; Yan, Jia-Jiun; Guh, Ying-Jey; Hayasaka, Oki; Lin, Li-Yih; Hwang, Pung-Pung; Wu, Guan-Chung; Chung, Ming-Tsung; Tseng, Yung-Che (2025): Seawater carbonate chemistry and transgenerational physiological and molecular data of Oryzias melastigma [dataset]. PANGAEA, https://doi.org/10.1594/PANGAEA.984450

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Published: 2025-08-22 • DOI registered: 2025-09-20

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Abstract:
To understand the long-term and transgenerational effects of marine fish, we applied a marine model animal, Oryzias melastigma, to a CO2-induced acidified condition (pH 7.6). This study focused on the larvae's physiological acclimation and how they face acidified stress through gene expression changes. Furthermore, we checked the epigenetic modifications, like DNA methylation, to know if there were any parental effects under this stress.
This dataset is included in the OA-ICC data compilation maintained in the framework of the IAEA Ocean Acidification International Coordination Centre (see https://oa-icc.ipsl.fr). Original data were downloaded from Dryad (see Source) by the OA-ICC data curator. In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2024) was used to compute a complete and consistent set of carbonate system variables, as described by Nisumaa et al. (2010). In this dataset the original values were archived in addition with the recalculated parameters (see related PI). The date of carbonate chemistry calculation by seacarb is 2025-08-21.
Keyword(s):
Animalia; Chordata; Gene expression (incl. proteomics); Growth/Morphology; Laboratory experiment; Laboratory strains; Nekton; Not applicable; Oryzias melastigma; Other metabolic rates; Other studied parameter or process; Pelagos; Respiration; Single species
Related to:
Liu, Tzu-Yen; Yan, Jia-Jiun; Guh, Ying-Jey; Hayasaka, Oki; Lin, Li-Yih; Hwang, Pung-Pung; Wu, Guan-Chung; Chung, Ming-Tsung; Tseng, Yung-Che (2025): Epigenetic insights into physiological resilience: Multigenerational readouts of CO2-induced seawater acidification effects on fish embryos. iScience, 28(9), 113187, https://doi.org/10.1016/j.isci.2025.113187
Source:
Liu, Tzu-Yen; Yan, Jia-Jiun; Hayasaka, Oki; Guh, Ying-Jey; Lin, Li-Yih; Wu, Guan-Chung; Chung, Ming-Tsung; Tseng, Yung-Che (2025): The transgenerational physiological and molecular data of Oryzias melastigma under seawater acidification stress [dataset]. Dryad, https://doi.org/10.5061/DRYAD.4XGXD25J7
References:
Nisumaa, Anne-Marin; Pesant, Stephane; Bellerby, Richard G J; Delille, Bruno; Middelburg, Jack J; Orr, James C; Riebesell, Ulf; Tyrrell, Toby; Wolf-Gladrow, Dieter A; Gattuso, Jean-Pierre (2010): EPOCA/EUR-OCEANS data compilation on the biological and biogeochemical responses to ocean acidification. Earth System Science Data, 2(2), 167-175, https://doi.org/10.5194/essd-2-167-2010
Yang, Yan; Brockmann, Patrick; Galdino, Carolina; Schindler, Uwe; Gazeau, Frédéric (2024): An update of data compilation on the biological response to ocean acidification and overview of the OA-ICC data portal. Earth System Science Data, 16(8), 3771-3780, https://doi.org/10.5194/essd-16-3771-2024
Yang, Yan; Hansson, L; Gattuso, Jean-Pierre (2016): Data compilation on the biological response to ocean acidification: an update. Earth System Science Data, 8(1), 79-87, https://doi.org/10.5194/essd-8-79-2016
Related code / software:
Gattuso, Jean-Pierre; Epitalon, Jean-Marie; Lavigne, Héloïse; Orr, James; Gentili, Bernard; Hagens, Mathilde; Hofmann, Andreas; Mueller, Jens-Daniel; Proye, Aurélien; Rae, James; Soetaert, Karline (2024): seacarb: seawater carbonate chemistry with R. R package version 3.3.3. https://cran.r-project.org/web/packages/seacarb/index.html
Project(s):
Ocean Acidification International Coordination Centre (OA-ICC)
Parameter(s):
#NameShort NameUnitPrincipal InvestigatorMethod/DeviceComment
1Type of studyStudy typeTseng, Yung-Che
2Species, unique identificationSpecies UIDTseng, Yung-Che
3Species, unique identification (URI)Species UID (URI)Tseng, Yung-Che
4Species, unique identification (Semantic URI)Species UID (Semantic URI)Tseng, Yung-Che
5Gene nameGeneTseng, Yung-Che
6Protein nameProteinTseng, Yung-Che
7GroupGroupTseng, Yung-CheWT=wildtype controls, F0, F1 and F2=three successive generations exposed to acidified conditions
8Gene expressionGene expressionTseng, Yung-Cherelative gene expression of acid-base regulation genes in each group
9DistanceDistanceµmTseng, Yung-CheInterocular
10Eye, diameterEye diammmTseng, Yung-Che
11Body lengthBLµmTseng, Yung-Chetotal
12HeighthµmTseng, Yung-CheBody
13WidthwµmTseng, Yung-CheBody
14StageStageTseng, Yung-Che
15Heart beat, frequencyHeart beat freqHzTseng, Yung-Che
16DNA methylation levelDNA methylation%Tseng, Yung-Che
17Oxygen consumption rateO2 conµmol/g/hTseng, Yung-Che
18Ammonium, excretion[NH4]+ excµmol/g/hTseng, Yung-Che
19Respiration rate/ammonia excretionO/NTseng, Yung-Che
20pH, NBS scalepH NBSTseng, Yung-Che
21pH, standard deviationpH std dev±Tseng, Yung-CheNBS scale
22Temperature, waterTemp°CTseng, Yung-Che
23Temperature, water, standard deviationTemp std dev±Tseng, Yung-Che
24SalinitySalTseng, Yung-Che
25Salinity, standard deviationSal std dev±Tseng, Yung-Che
26Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)pCO2water_SST_wetµatmTseng, Yung-CheCalculated using CO2SYS
27Partial pressure of carbon dioxide, standard deviationpCO2 std dev±Tseng, Yung-CheCalculated using CO2SYS
28Carbon, inorganic, dissolvedDICµmol/kgTseng, Yung-Che
29Carbon, inorganic, dissolved, standard deviationDIC std dev±Tseng, Yung-Che
30Alkalinity, totalATµmol/kgTseng, Yung-Che
31Alkalinity, total, standard deviationAT std dev±Tseng, Yung-Che
32Carbonate system computation flagCSC flagYang, YanCalculated using seacarb after Nisumaa et al. (2010)
33pH, total scalepHTYang, YanCalculated using seacarb after Nisumaa et al. (2010)
34pH, standard deviationpH std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
35Carbon dioxideCO2µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
36Carbon dioxide, standard deviationCO2 std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
37Fugacity of carbon dioxide (water) at sea surface temperature (wet air)fCO2water_SST_wetµatmYang, YanCalculated using seacarb after Nisumaa et al. (2010)
38Fugacity of carbon dioxide in seawater, standard deviationfCO2 std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
39Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)pCO2water_SST_wetµatmYang, YanCalculated using seacarb after Nisumaa et al. (2010)
40Partial pressure of carbon dioxide, standard deviationpCO2 std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
41Bicarbonate ion[HCO3]-µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
42Bicarbonate ion, standard deviation[HCO3]- std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
43Carbonate ion[CO3]2-µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
44Carbonate ion, standard deviation[CO3]2- std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
45Aragonite saturation stateOmega ArgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
46Aragonite saturation state, standard deviationOmega Arg std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
47Calcite saturation stateOmega CalYang, YanCalculated using seacarb after Nisumaa et al. (2010)
48Calcite saturation state, standard deviationOmega Cal std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
License:
Creative Commons Attribution 4.0 International (CC-BY-4.0)
Status:
Curation Level: Enhanced curation (CurationLevelC)
Size:
26432 data points

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