Citation:

PANGAEA.985486

Name: Seawater carbonate chemistry and circadian splicing patterns in the brain of fish
Published: 2025-09-18
License: https://creativecommons.org/licenses/by/4.0/
Keywords: Acanthochromis polyacanthus; Animalia; Chordata; Coast and continental shelf; Containers and aquaria (20-1000 L or < 1 m**2); Gene expression (incl. proteomics); Laboratory experiment; Nekton; Pelagos; Single species; South Pacific; Tropical

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Published: 2025-09-18 • DOI registered: 2025-10-22

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Abstract:

In this study, we examine the transcriptional patterns mediated by alternative splicing in driving the molecular response of fish to OA across their daily cycle. We assess the impact of environmental CO2 variation at four timepoints throughout a circadian (24-hr) day and aim to: (1) determine if the temporal patterns of splicing events in the brain in control conditions are altered by exposure to near-future predicted CO2 levels, and (2) gain a comprehensive understanding of splicing patterns under stable and fluctuating CO2 conditions by conducting pairwise comparisons between control and each CO2 condition separately for each time point. We reveal how splicing events may facilitate regulation of biological responses of fish to environmental CO2 variability across a circadian timeline.

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 carbonate chemistry data were downloaded from the PANGAEA dataset (see Source). In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2019) 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 2020-02-28.

Keyword(s):

Acanthochromis polyacanthus; Animalia; Chordata; Coast and continental shelf; Containers and aquaria (20-1000 L or < 1 m**2); Gene expression (incl. proteomics); Laboratory experiment; Nekton; Pelagos; Single species; South Pacific; Tropical

Related to:

Suresh, Sneha; Jarrold, Michael; Ravasi, Timothy; Munday, Philip L; Schunter, Celia (2025): Ocean acidification induces changes in circadian alternative splicing profiles in a coral reef fish. Scientific Reports, 15(1), 22107, https://doi.org/10.1038/s41598-025-06786-0

Source:

Jarrold, Michael; Munday, Philip L (2018): Seawater carbonate chemistry and survival, growth and behavior of a coral reef fish [dataset]. PANGAEA, https://doi.org/10.1594/PANGAEA.912848

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 C; Gentili, Bernard; Hagens, Mathilde; Hofmann, Andreas; Mueller, Jens-Daniel; Proye, Aurélien; Rae, James; Soetaert, Karline (2019): seacarb: seawater carbonate chemistry with R. R package version 3.2.12. https://CRAN.R-project.org/package=seacarb

Further details:

Suresh, Sneha: Alternative and differnetial splicing events. Alternative and differnetial splicing events.xlsx

Project(s):

Ocean Acidification International Coordination Centre (OA-ICC)

Coverage:

Latitude: -18.829000 * Longitude: 147.656000

Date/Time Start: 2017-07-01T00:00:00 * Date/Time End: 2017-08-31T00:00:00

Event(s):

Davies_Reef_fish * Latitude: -18.829000 * Longitude: 147.656000 * Date/Time Start: 2017-07-01T00:00:00 * Date/Time End: 2017-08-31T00:00:00 * Method/Device: Experiment (EXP)

Parameter(s):

#	Name	Short Name	Unit	Principal Investigator	Method/Device	Comment
1	Type of study	Study type		Jarrold, Michael
2	Species, unique identification	Species UID		Jarrold, Michael
3	Species, unique identification (URI)	Species UID (URI)		Jarrold, Michael
4	Species, unique identification (Semantic URI)	Species UID (Semantic URI)		Jarrold, Michael
5	Treatment	Treat		Jarrold, Michael		pCO2
6	Treatment: temperature	T:temp	°C	Jarrold, Michael
7	Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)	pCO2water_SST_wet	µatm	Jarrold, Michael		mean
8	Partial pressure of carbon dioxide, standard deviation	pCO2 std dev	±	Jarrold, Michael		mean
9	Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)	pCO2water_SST_wet	µatm	Jarrold, Michael		min
10	Partial pressure of carbon dioxide, standard deviation	pCO2 std dev	±	Jarrold, Michael		min
11	Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)	pCO2water_SST_wet	µatm	Jarrold, Michael		max
12	Partial pressure of carbon dioxide, standard deviation	pCO2 std dev	±	Jarrold, Michael		max
13	Temperature, water	Temp	°C	Jarrold, Michael
14	Temperature, water, standard deviation	Temp std dev	±	Jarrold, Michael
15	Salinity	Sal		Jarrold, Michael
16	Salinity, standard deviation	Sal std dev	±	Jarrold, Michael
17	Alkalinity, total	AT	µmol/kg	Jarrold, Michael
18	Alkalinity, total, standard deviation	AT std dev	±	Jarrold, Michael
19	Carbonate system computation flag	CSC flag		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
20	pH, total scale	pHT		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	mean
21	pH, standard deviation	pH std dev	±	Yang, Yan	Calculated using seacarb after Orr et al. (2018)	mean
22	Carbon dioxide	CO2	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	mean
23	Carbon dioxide, standard deviation	CO2 std dev	±	Yang, Yan	Calculated using seacarb after Orr et al. (2018)	mean
24	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)	mean
25	Fugacity of carbon dioxide in seawater, standard deviation	fCO2 std dev	±	Yang, Yan	Calculated using seacarb after Orr et al. (2018)	mean
26	Bicarbonate ion	[HCO3]-	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	mean
27	Bicarbonate ion, standard deviation	[HCO3]- std dev	±	Yang, Yan	Calculated using seacarb after Orr et al. (2018)	mean
28	Carbonate ion	[CO3]2-	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	mean
29	Carbonate ion, standard deviation	[CO3]2- std dev	±	Yang, Yan	Calculated using seacarb after Orr et al. (2018)	mean
30	Carbon, inorganic, dissolved	DIC	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	mean
31	Carbon, inorganic, dissolved, standard deviation	DIC std dev	±	Yang, Yan	Calculated using seacarb after Orr et al. (2018)	mean
32	Aragonite saturation state	Omega Arg		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	mean
33	Aragonite saturation state, standard deviation	Omega Arg std dev	±	Yang, Yan	Calculated using seacarb after Orr et al. (2018)	mean
34	Calcite saturation state	Omega Cal		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	mean
35	Calcite saturation state, standard deviation	Omega Cal std dev	±	Yang, Yan	Calculated using seacarb after Orr et al. (2018)	mean

License:

Creative Commons Attribution 4.0 International (CC-BY-4.0)

Status:

Curation Level: Enhanced curation (CurationLevelC)

Size:

264 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 Treat (pCO2)	6 T:temp [°C]	7 pCO2water_SST_wet [µatm] (mean)	8 pCO2 std dev [±] (mean)	9 pCO2water_SST_wet [µatm] (min)	10 pCO2 std dev [±] (min)	11 pCO2water_SST_wet [µatm] (max)	12 pCO2 std dev [±] (max)	13 Temp [°C]	14 Temp std dev [±]	15 Sal	16 Sal std dev [±]	17 AT [µmol/kg]	18 AT std dev [±]	19 CSC flag (Calculated using seacarb afte...)	20 pHT (mean, Calculated using seacar...)	21 pH std dev [±] (mean, Calculated using seacar...)	22 CO2 [µmol/kg] (mean, Calculated using seacar...)	23 CO2 std dev [±] (mean, Calculated using seacar...)	24 fCO2water_SST_wet [µatm] (mean, Calculated using seacar...)	25 fCO2 std dev [±] (mean, Calculated using seacar...)	26 [HCO3]- [µmol/kg] (mean, Calculated using seacar...)	27 [HCO3]- std dev [±] (mean, Calculated using seacar...)	28 [CO3]2- [µmol/kg] (mean, Calculated using seacar...)	29 [CO3]2- std dev [±] (mean, Calculated using seacar...)	30 DIC [µmol/kg] (mean, Calculated using seacar...)	31 DIC std dev [±] (mean, Calculated using seacar...)	32 Omega Arg (mean, Calculated using seacar...)	33 Omega Arg std dev [±] (mean, Calculated using seacar...)	34 Omega Cal (mean, Calculated using seacar...)	35 Omega Cal std dev [±] (mean, Calculated using seacar...)
laboratory	Acanthochromis polyacanthus	marinespecies.org	urn:lsid:marinespecies.org:taxname:279469	450	29	435	38	425	36	477	163	28.8	0.2	35.4	0.4	2325	33	24	8.01	0.03	11.2	0.98	433.67	37.88	1766.14	38.73	227.92	14.59	2005.26	33.26	3.68	0.29	5.51	0.43
laboratory	Acanthochromis polyacanthus	marinespecies.org	urn:lsid:marinespecies.org:taxname:279469	450	31	475	44	459	31	527	224	31.1	0.3	35.4	0.4	2306	51	24	7.98	0.03	11.6	1.08	473.59	43.87	1751.97	47.15	225.83	16.44	1989.41	46.15	3.69	0.32	5.48	0.47
laboratory	Acanthochromis polyacanthus	marinespecies.org	urn:lsid:marinespecies.org:taxname:279469	1000	29	992	19	956	74	1035	95	28.8	0.2	35.4	0.4	2325	32	24	7.71	0.01	25.5	0.52	988.97	18.94	2009.03	26.76	129.33	5.51	2163.90	28.72	2.09	0.13	3.12	0.20
laboratory	Acanthochromis polyacanthus	marinespecies.org	urn:lsid:marinespecies.org:taxname:279469	1000	31	981	8	958	42	1002	23	31.1	0.3	35.4	0.4	2310	48	24	7.71	0.01	24.0	0.28	978.09	7.98	1971.64	37.88	138.49	6.81	2134.10	42.17	2.26	0.15	3.36	0.23
laboratory	Acanthochromis polyacanthus	marinespecies.org	urn:lsid:marinespecies.org:taxname:279469	1000±300	29	1009	25	653	25	1329	89	28.8	0.2	35.4	0.4	2318	38	24	7.70	0.01	26.0	0.67	1005.92	24.92	2007.63	31.45	126.97	6.00	2160.58	34.06	2.05	0.14	3.07	0.20
laboratory	Acanthochromis polyacanthus	marinespecies.org	urn:lsid:marinespecies.org:taxname:279469	1000±300	31	1034	33	668	27	1349	97	31.1	0.3	35.4	0.4	2318	36	24	7.69	0.02	25.3	0.83	1030.93	32.90	1990.95	30.26	133.98	6.52	2150.18	32.39	2.19	0.15	3.25	0.22
laboratory	Acanthochromis polyacanthus	marinespecies.org	urn:lsid:marinespecies.org:taxname:279469	1000±500	29	1060	34	521	43	1544	80	28.8	0.2	35.4	0.4	2323	32	24	7.68	0.02	27.3	0.89	1056.77	33.90	2023.14	27.58	122.74	5.82	2173.18	29.16	1.98	0.13	2.97	0.20
laboratory	Acanthochromis polyacanthus	marinespecies.org	urn:lsid:marinespecies.org:taxname:279469	1000±500	31	1079	49	556	64	1570	118	31.1	0.3	35.4	0.4	2314	39	24	7.68	0.02	26.4	1.22	1075.80	48.85	1998.24	33.45	129.33	7.25	2153.93	35.48	2.11	0.15	3.14	0.23