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Schwaner, Caroline; Farhat, Sarah; Barbosa, Michelle; Boutet, Isabelle; Tanguy, Arnaud; Espinosa, Emmanuelle Pales; Allam, Bassem (2024): Seawater carbonate chemistry and cellular and alterations in gene expression in Mercenaria mercenaria [dataset]. PANGAEA, https://doi.org/10.1594/PANGAEA.967053

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Abstract:
Northern quahog (Mercenaria mercenaria) were fertilized under normal pCO2 and reared under acidified (pH ~ 7.5, pCO2 ~ 1200 ppm) or control (pH ~ 7.9, pCO2 ~ 600 ppm) conditions before sampled at 2 days (larvae), 32 days (postsets), 5 and 10 months (juveniles) and submitted to RNA and DNA sequencing to evaluate alterations in gene expression and genetic variations.
Keyword(s):
Animalia; Benthic animals; Benthos; Coast and continental shelf; Containers and aquaria (20-1000 L or < 1 m**2); Gene expression (incl. proteomics); Laboratory experiment; Mercenaria mercenaria; Mollusca; North Atlantic; Pelagos; Single species; Temperate; Zooplankton
Related to:
Schwaner, Caroline; Farhat, Sarah; Barbosa, Michelle; Boutet, Isabelle; Tanguy, Arnaud; Espinosa, Emmanuelle Pales; Allam, Bassem (2023): Molecular Features Associated with Resilience to Ocean Acidification in the Northern Quahog, Mercenaria mercenaria. Marine Biotechnology, 25(1), 83-99, https://doi.org/10.1007/s10126-022-10183-3
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 (2022): seacarb: seawater carbonate chemistry with R. R package version 3.3.1. https://cran.r-project.org/web/packages/seacarb/index.html
Project(s):
Ocean Acidification International Coordination Centre (OA-ICC)
Coverage:
Median Latitude: 41.154350 * Median Longitude: -72.138450 * South-bound Latitude: 40.869000 * West-bound Longitude: -73.343200 * North-bound Latitude: 41.930500 * East-bound Longitude: -70.031000
Event(s):
Hampton_Bays * Latitude: 40.869000 * Longitude: -72.517600 * Method/Device: Experiment (EXP)
Northport * Latitude: 40.900900 * Longitude: -73.343200 * Method/Device: Experiment (EXP)
Riverhead_OA * Latitude: 40.917000 * Longitude: -72.662000 * Method/Device: Experiment (EXP)
Comment:
In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2022) 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 2023-04-23.
Parameter(s):
#NameShort NameUnitPrincipal InvestigatorMethod/DeviceComment
1Type of studyStudy typeAllam, Bassem
2Species, unique identificationSpecies UIDAllam, Bassem
3Species, unique identification (URI)Species UID (URI)Allam, Bassem
4Species, unique identification (Semantic URI)Species UID (Semantic URI)Allam, Bassem
5Time point, descriptiveTime pointAllam, Bassem
6TreatmentTreatAllam, Bassem
7Numbern#Allam, BassemDiferentially expressed gene
8Numbern#Allam, BassemUpregulated genes
9PercentagePerc%Allam, BassemUpregulated genes
10Numbern#Allam, BassemDownregulated genes
11PercentagePerc%Allam, BassemDownregulated genes
12Temperature, waterTemp°CAllam, Bassem
13Temperature, water, standard deviationTemp std dev±Allam, Bassem
14pHpHAllam, Bassemtotal scale
15pH, standard deviationpH std dev±Allam, Bassemtotal scale
16Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)pCO2water_SST_wetµatmAllam, Bassem
17Partial pressure of carbon dioxide, standard deviationpCO2 std dev±Allam, Bassem
18Calcite saturation stateOmega CalAllam, Bassem
19Calcite saturation state, standard deviationOmega Cal std dev±Allam, Bassem
20Aragonite saturation stateOmega ArgAllam, Bassem
21Aragonite saturation state, standard deviationOmega Arg std dev±Allam, Bassem
22Carbon, inorganic, dissolvedDICµmol/kgAllam, Bassem
23Carbon, inorganic, dissolved, standard deviationDIC std dev±Allam, Bassem
24Carbonate ion[CO3]2-µmol/kgAllam, Bassem
25Carbonate ion, standard deviation[CO3]2- std dev±Allam, Bassem
26Alkalinity, totalATµmol/kgAllam, Bassem
27Alkalinity, total, standard deviationAT std dev±Allam, Bassem
28SalinitySalAllam, Bassem
29Salinity, standard deviationSal std dev±Allam, Bassem
30Carbonate system computation flagCSC flagYang, YanCalculated using seacarb after Nisumaa et al. (2010)
31Carbon dioxideCO2µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
32Carbon dioxide, standard deviationCO2 std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
33Fugacity of carbon dioxide (water) at sea surface temperature (wet air)fCO2water_SST_wetµatmYang, YanCalculated using seacarb after Nisumaa et al. (2010)
34Fugacity of carbon dioxide in seawater, standard deviationfCO2 std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
35Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)pCO2water_SST_wetµatmYang, YanCalculated using seacarb after Nisumaa et al. (2010)
36Partial pressure of carbon dioxide, standard deviationpCO2 std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
37Bicarbonate ion[HCO3]-µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
38Bicarbonate ion, standard deviation[HCO3]- std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
39Carbonate ion[CO3]2-µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
40Carbonate ion, standard deviation[CO3]2- std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
41Carbon, inorganic, dissolvedDICµmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
42Carbon, inorganic, dissolved, standard deviationDIC std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
43Aragonite saturation stateOmega ArgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
44Aragonite saturation state, standard deviationOmega Arg std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
45Calcite saturation stateOmega CalYang, YanCalculated using seacarb after Nisumaa et al. (2010)
46Calcite 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:
332 data points

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