Citation:

PANGAEA.967053

Name: Seawater carbonate chemistry and cellular and alterations in gene expression in Mercenaria mercenaria
Published: 2024-03-26
License: https://creativecommons.org/licenses/by/4.0/
Keywords: 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

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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):

#	Name	Short Name	Unit	Principal Investigator	Method/Device	Comment
1	Type of study	Study type		Allam, Bassem
2	Species, unique identification	Species UID		Allam, Bassem
3	Species, unique identification (URI)	Species UID (URI)		Allam, Bassem
4	Species, unique identification (Semantic URI)	Species UID (Semantic URI)		Allam, Bassem
5	Time point, descriptive	Time point		Allam, Bassem
6	Treatment	Treat		Allam, Bassem
7	Number	n	#	Allam, Bassem		Diferentially expressed gene
8	Number	n	#	Allam, Bassem		Upregulated genes
9	Percentage	Perc	%	Allam, Bassem		Upregulated genes
10	Number	n	#	Allam, Bassem		Downregulated genes
11	Percentage	Perc	%	Allam, Bassem		Downregulated genes
12	Temperature, water	Temp	°C	Allam, Bassem
13	Temperature, water, standard deviation	Temp std dev	±	Allam, Bassem
14	pH	pH		Allam, Bassem		total scale
15	pH, standard deviation	pH std dev	±	Allam, Bassem		total scale
16	Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)	pCO2water_SST_wet	µatm	Allam, Bassem
17	Partial pressure of carbon dioxide, standard deviation	pCO2 std dev	±	Allam, Bassem
18	Calcite saturation state	Omega Cal		Allam, Bassem
19	Calcite saturation state, standard deviation	Omega Cal std dev	±	Allam, Bassem
20	Aragonite saturation state	Omega Arg		Allam, Bassem
21	Aragonite saturation state, standard deviation	Omega Arg std dev	±	Allam, Bassem
22	Carbon, inorganic, dissolved	DIC	µmol/kg	Allam, Bassem
23	Carbon, inorganic, dissolved, standard deviation	DIC std dev	±	Allam, Bassem
24	Carbonate ion	[CO3]2-	µmol/kg	Allam, Bassem
25	Carbonate ion, standard deviation	[CO3]2- std dev	±	Allam, Bassem
26	Alkalinity, total	AT	µmol/kg	Allam, Bassem
27	Alkalinity, total, standard deviation	AT std dev	±	Allam, Bassem
28	Salinity	Sal		Allam, Bassem
29	Salinity, standard deviation	Sal std dev	±	Allam, Bassem
30	Carbonate system computation flag	CSC flag		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
31	Carbon dioxide	CO2	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
32	Carbon dioxide, standard deviation	CO2 std dev	±	Yang, Yan	Calculated using seacarb after Orr et al. (2018)
33	Fugacity of carbon dioxide (water) at sea surface temperature (wet air)	fCO2water_SST_wet	µatm	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
34	Fugacity of carbon dioxide in seawater, standard deviation	fCO2 std dev	±	Yang, Yan	Calculated using seacarb after Orr et al. (2018)
35	Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)	pCO2water_SST_wet	µatm	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
36	Partial pressure of carbon dioxide, standard deviation	pCO2 std dev	±	Yang, Yan	Calculated using seacarb after Orr et al. (2018)
37	Bicarbonate ion	[HCO3]-	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
38	Bicarbonate ion, standard deviation	[HCO3]- std dev	±	Yang, Yan	Calculated using seacarb after Orr et al. (2018)
39	Carbonate ion	[CO3]2-	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
40	Carbonate ion, standard deviation	[CO3]2- std dev	±	Yang, Yan	Calculated using seacarb after Orr et al. (2018)
41	Carbon, inorganic, dissolved	DIC	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
42	Carbon, inorganic, dissolved, standard deviation	DIC std dev	±	Yang, Yan	Calculated using seacarb after Orr et al. (2018)
43	Aragonite saturation state	Omega Arg		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
44	Aragonite saturation state, standard deviation	Omega Arg std dev	±	Yang, Yan	Calculated using seacarb after Orr et al. (2018)
45	Calcite saturation state	Omega Cal		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
46	Calcite saturation state, standard deviation	Omega Cal std dev	±	Yang, Yan	Calculated 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

Data

Download dataset as tab-delimited text — use the following character encoding:

1 Study type	2 Species UID	3 Species UID (URI)	4 Species UID (Semantic URI)	5 Time point	6 Treat	7 n [#] (Diferentially expressed gene)	8 n [#] (Upregulated genes)	9 Perc [%] (Upregulated genes)	10 n [#] (Downregulated genes)	11 Perc [%] (Downregulated genes)	12 Temp [°C]	13 Temp std dev [±]	14 pH (total scale)	15 pH std dev [±] (total scale)	16 pCO2water_SST_wet [µatm]	17 pCO2 std dev [±]	18 Omega Cal	19 Omega Cal std dev [±]	20 Omega Arg	21 Omega Arg std dev [±]	22 DIC [µmol/kg]	23 DIC std dev [±]	24 [CO3]2- [µmol/kg]	25 [CO3]2- std dev [±]	26 AT [µmol/kg]	27 AT std dev [±]	28 Sal	29 Sal std dev [±]	30 CSC flag (Calculated using seacarb afte...)	31 CO2 [µmol/kg] (Calculated using seacarb afte...)	32 CO2 std dev [±] (Calculated using seacarb afte...)	33 fCO2water_SST_wet [µatm] (Calculated using seacarb afte...)	34 fCO2 std dev [±] (Calculated using seacarb afte...)	35 pCO2water_SST_wet [µatm] (Calculated using seacarb afte...)	36 pCO2 std dev [±] (Calculated using seacarb afte...)	37 [HCO3]- [µmol/kg] (Calculated using seacarb afte...)	38 [HCO3]- std dev [±] (Calculated using seacarb afte...)	39 [CO3]2- [µmol/kg] (Calculated using seacarb afte...)	40 [CO3]2- std dev [±] (Calculated using seacarb afte...)	41 DIC [µmol/kg] (Calculated using seacarb afte...)	42 DIC std dev [±] (Calculated using seacarb afte...)	43 Omega Arg (Calculated using seacarb afte...)	44 Omega Arg std dev [±] (Calculated using seacarb afte...)	45 Omega Cal (Calculated using seacarb afte...)	46 Omega Cal std dev [±] (Calculated using seacarb afte...)
laboratory	Mercenaria mercenaria	marinespecies.org	urn:lsid:marinespecies.org:taxname:141919	2 day old larval clams	Control						21.30	0.00	7.80	0.00	634.990	2.71	2.14	0.01	1.38	0.01	1739.73	7.13	86.18	0.48	1850.31	7.60	30.00	0.00	9	20.55	0.36	639.69	11.66	641.83	11.70	1633.08	7.26	86.10	2.85	1850.03	8.03	1.38	0.08	2.14	0.12
laboratory	Mercenaria mercenaria	marinespecies.org	urn:lsid:marinespecies.org:taxname:141919	2 day old larval clams	Acidified	61	26	42.6	35	57.4	21.30	0.00	7.50	0.00	1255.780	185.69	1.06	0.16	0.69	0.10	1701.62	251.19	42.82	6.40	1727.96	251.73	30.00	0.00	9	40.63	6.04	1264.74	188.01	1268.98	188.64	1618.23	238.89	42.76	6.47	1727.48	251.51	0.68	0.11	1.06	0.17
laboratory	Mercenaria mercenaria	marinespecies.org	urn:lsid:marinespecies.org:taxname:141919	32 day old juvenile clams	Control						21.16	0.03	7.89	0.03	576.040	124.04	2.94	0.65	1.90	0.42	1909.11	59.95	120.15	26.95	2068.84	99.70	31.91	0.80	9	17.82	1.45	558.33	45.36	560.20	45.51	1771.40	56.14	119.89	9.52	2069.27	64.54	1.90	0.17	2.94	0.27
laboratory	Mercenaria mercenaria	marinespecies.org	urn:lsid:marinespecies.org:taxname:141919	32 day old juvenile clams	Acidified	108	9	83.3	99	91.7	21.20	0.03	7.57	0.02	1166.263	158.10	1.58	0.25	1.02	0.17	1978.18	92.80	64.50	10.99	2036.88	104.90	32.06	0.60	9	39.38	2.69	1236.01	84.53	1240.16	84.82	1877.66	88.11	61.14	4.49	2030.10	94.04	0.97	0.08	1.50	0.13
laboratory	Mercenaria mercenaria	marinespecies.org	urn:lsid:marinespecies.org:taxname:141919	5 month old clams	Control						21.16	0.06	7.96	0.01	482.210	15.13	3.71	0.13	2.42	0.09	1980.51	6.49	154.97	550.00	2195.74	14.60	35.00	0.00	9	15.08	0.46	480.49	14.74	482.10	14.79	1810.50	8.24	154.92	5.97	2195.72	10.18	2.42	0.15	3.71	0.22
laboratory	Mercenaria mercenaria	marinespecies.org	urn:lsid:marinespecies.org:taxname:141919	5 month old clams	Acidified	170	112	65.9	58	34.1	21.10	0.08	7.63	0.01	1134.570	38.97	1.91	0.06	1.24	0.04	2108.27	3.26	79.61	2.66	2190.85	1.95	35.00	0.00	9	35.55	1.04	1130.46	33.27	1134.26	33.38	1993.13	4.19	79.59	3.21	2190.85	5.64	1.24	0.08	1.91	0.12
laboratory	Mercenaria mercenaria	marinespecies.org	urn:lsid:marinespecies.org:taxname:141919	10 month old clams	Control						21.17	0.14	7.91	0.06	543.210	71.52	3.02	0.29	1.95	0.18	1980.51	6.49	122.01	10.10	2071.58	43.60	30.63	2.26	9	17.87	2.62	556.14	81.66	558.00	81.93	1836.51	15.66	126.13	16.99	2146.00	27.14	2.01	0.29	3.12	0.44
laboratory	Mercenaria mercenaria	marinespecies.org	urn:lsid:marinespecies.org:taxname:141919	10 month old clams	Acidified	20	4	20.0	16	80.0	21.23	0.09	7.53	0.03	1344.380	90.69	1.35	0.13	0.87	0.08	2108.27	3.26	54.95	5.27	1993.83	66.93	31.62	1.64	9	46.23	3.31	1448.86	103.87	1453.73	104.22	2003.13	3.82	58.91	4.51	2148.12	9.87	0.94	0.08	1.45	0.13