Citation:

PANGAEA.920153

Name: Seawater carbonate chemistry and gene expression in the gills of juvenile turbot (Psetta maxima)
Published: 2019
License: https://creativecommons.org/licenses/by/4.0/
Keywords: Animalia; Chordata; Coast and continental shelf; Containers and aquaria (20-1000 L or < 1 m**2); Gene expression (incl. proteomics); Laboratory experiment; Nekton; North Atlantic; Other studied parameter or process; Pelagos; Psetta maxima; Single species; Temperate

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Abstract:

The data sets stem from a study which aimed to investigate the impact of chronic severe hypercapnia on the cellular stress response in the gills of juvenile turbot (Psetta maxima). The experiment was conducted in the so called respirometer, a recirculating aquaculture respirometer system (RARS) which allowed the persistent, stable manipulation of carbon dioxide concentrations. Juvenile turbot (Psetta maxima) where subjected to different levels of environmental hypercapnia (low: ~3000 μatm, medium: ~15000 μatm, high: ~25000 μatm). After eight weeks, fish where sacrificed and gill samples were taken for further histological and transcriptional analysis. For histological investigation of the gills, samples where fixed in 4% phosphate-buffered formalin and examined via a microscope equipped with a digital camera. In order to investigate changes in the transcriptome, a fraction of the gill samples was stored in RNAlater. Relative gene expression analysis was conducted via RT-qPCR, using a Fluidigm chip system. Calibrated normalized relative quantities (CNRQs) where assessed with the QBASE software. This included the evaluation of the most suitable combination of reference genes with the help of the GeNorm algorithm.

Keyword(s):

Animalia; Chordata; Coast and continental shelf; Containers and aquaria (20-1000 L or < 1 m**2); Gene expression (incl. proteomics); Laboratory experiment; Nekton; North Atlantic; Other studied parameter or process; Pelagos; Psetta maxima; Single species; Temperate

Related to:

Hermann, Bernd Timo; Würtz, Sven; Vanselow, Klaus Heinrich; Schulz, Carsten; Stiller, Kevin Torben (2019): Divergent gene expression in the gills of juvenile turbot (Psetta maxima) exposed to chronic severe hypercapnia indicates dose-dependent increase in intracellular oxidative stress and hypoxia. Aquatic Toxicology, 206, 72-80, https://doi.org/10.1016/j.aquatox.2018.10.023

Original version:

Hermann, Bernd Timo; Würtz, Sven; Vanselow, Klaus Heinrich; Schulz, Carsten; Stiller, Kevin Torben (2018): Histological and relative gene expression data obtained from the gills of juvenile turbot (Psetta maxima) after the exposure to varying degrees of severe environmental hypercapnia for 8 weeks. PANGAEA, https://doi.org/10.1594/PANGAEA.893884

Further details:

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

Project(s):

Ocean Acidification International Coordination Centre (OA-ICC)

Comment:

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 2020-07-07.

Parameter(s):

#	Name	Short Name	Unit	Principal Investigator	Method/Device	Comment
1	Type	Type		Hermann, Bernd Timo		study
2	Species	Species		Hermann, Bernd Timo
3	Registration number of species	Reg spec no		Hermann, Bernd Timo
4	Uniform resource locator/link to reference	URL ref		Hermann, Bernd Timo		WoRMS Aphia ID
5	Experiment duration	Exp duration	days	Hermann, Bernd Timo
6	Sample type	Samp type		Hermann, Bernd Timo
7	Sample ID	Sample ID		Hermann, Bernd Timo
8	Treatment	Treat		Hermann, Bernd Timo
9	Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)	pCO2water_SST_wet	µatm	Hermann, Bernd Timo
10	Replicate	Repl		Hermann, Bernd Timo
11	CNRQs, Quantitative reverse transcription PCR	RT-qPCR		Hermann, Bernd Timo	Quantitative reverse transcription polymerase chain reaction (qRT-PCR)	Adenylat Kinase 2
12	CNRQs, Quantitative reverse transcription PCR	RT-qPCR		Hermann, Bernd Timo	Quantitative reverse transcription polymerase chain reaction (qRT-PCR)	Akirin
13	CNRQs, Quantitative reverse transcription PCR	RT-qPCR		Hermann, Bernd Timo	Quantitative reverse transcription polymerase chain reaction (qRT-PCR)	Apolipoprotein E
14	CNRQs, Quantitative reverse transcription PCR	RT-qPCR		Hermann, Bernd Timo	Quantitative reverse transcription polymerase chain reaction (qRT-PCR)	Arginase
15	CNRQs, Quantitative reverse transcription PCR	RT-qPCR		Hermann, Bernd Timo	Quantitative reverse transcription polymerase chain reaction (qRT-PCR)	Cathepsin D
16	CNRQs, Quantitative reverse transcription PCR	RT-qPCR		Hermann, Bernd Timo	Quantitative reverse transcription polymerase chain reaction (qRT-PCR)	Copper Chaperone
17	CNRQs, Quantitative reverse transcription PCR	RT-qPCR		Hermann, Bernd Timo	Quantitative reverse transcription polymerase chain reaction (qRT-PCR)	Cytochrome C Oxidase
18	CNRQs, Quantitative reverse transcription PCR	RT-qPCR		Hermann, Bernd Timo	Quantitative reverse transcription polymerase chain reaction (qRT-PCR)	Cystatin B
19	CNRQs, Quantitative reverse transcription PCR	RT-qPCR		Hermann, Bernd Timo	Quantitative reverse transcription polymerase chain reaction (qRT-PCR)	Cytochrome P450
20	CNRQs, Quantitative reverse transcription PCR	RT-qPCR		Hermann, Bernd Timo	Quantitative reverse transcription polymerase chain reaction (qRT-PCR)	delta_6-Fatty acid Desaturase
21	CNRQs, Quantitative reverse transcription PCR	RT-qPCR		Hermann, Bernd Timo	Quantitative reverse transcription polymerase chain reaction (qRT-PCR)	Elongation Factor 1 alpha
22	CNRQs, Quantitative reverse transcription PCR	RT-qPCR		Hermann, Bernd Timo	Quantitative reverse transcription polymerase chain reaction (qRT-PCR)	Polyunsaturated fatty acid elongase
23	CNRQs, Quantitative reverse transcription PCR	RT-qPCR		Hermann, Bernd Timo	Quantitative reverse transcription polymerase chain reaction (qRT-PCR)	growth arrest and DNA-damage inducible protein 45 alpha
24	CNRQs, Quantitative reverse transcription PCR	RT-qPCR		Hermann, Bernd Timo	Quantitative reverse transcription polymerase chain reaction (qRT-PCR)	growth hormone receptor
25	CNRQs, Quantitative reverse transcription PCR	RT-qPCR		Hermann, Bernd Timo	Quantitative reverse transcription polymerase chain reaction (qRT-PCR)	Cell death-regulatory protein
26	CNRQs, Quantitative reverse transcription PCR	RT-qPCR		Hermann, Bernd Timo	Quantitative reverse transcription polymerase chain reaction (qRT-PCR)	Glutathione-S-Transferase
27	CNRQs, Quantitative reverse transcription PCR	RT-qPCR		Hermann, Bernd Timo	Quantitative reverse transcription polymerase chain reaction (qRT-PCR)	3-Hydroxy-3Methylglutaryl-Coenzym A Reductase
28	CNRQs, Quantitative reverse transcription PCR	RT-qPCR		Hermann, Bernd Timo	Quantitative reverse transcription polymerase chain reaction (qRT-PCR)	Heat Shock Protein 40kDa
29	CNRQs, Quantitative reverse transcription PCR	RT-qPCR		Hermann, Bernd Timo	Quantitative reverse transcription polymerase chain reaction (qRT-PCR)	Heat Shock Protein 70kDa
30	CNRQs, Quantitative reverse transcription PCR	RT-qPCR		Hermann, Bernd Timo	Quantitative reverse transcription polymerase chain reaction (qRT-PCR)	Heat Shock Protein 90kDa
31	CNRQs, Quantitative reverse transcription PCR	RT-qPCR		Hermann, Bernd Timo	Quantitative reverse transcription polymerase chain reaction (qRT-PCR)	Insulin-like growth factor 1
32	CNRQs, Quantitative reverse transcription PCR	RT-qPCR		Hermann, Bernd Timo	Quantitative reverse transcription polymerase chain reaction (qRT-PCR)	Insulin-like growth factor 2
33	CNRQs, Quantitative reverse transcription PCR	RT-qPCR		Hermann, Bernd Timo	Quantitative reverse transcription polymerase chain reaction (qRT-PCR)	Interleukin-1 beta
34	CNRQs, Quantitative reverse transcription PCR	RT-qPCR		Hermann, Bernd Timo	Quantitative reverse transcription polymerase chain reaction (qRT-PCR)	Interferone regulatory factor 3
35	CNRQs, Quantitative reverse transcription PCR	RT-qPCR		Hermann, Bernd Timo	Quantitative reverse transcription polymerase chain reaction (qRT-PCR)	Interferone regulatory factor 5
36	CNRQs, Quantitative reverse transcription PCR	RT-qPCR		Hermann, Bernd Timo	Quantitative reverse transcription polymerase chain reaction (qRT-PCR)	Interferone regulatory factor 7
37	CNRQs, Quantitative reverse transcription PCR	RT-qPCR		Hermann, Bernd Timo	Quantitative reverse transcription polymerase chain reaction (qRT-PCR)	Low molecular weight polypeptide
38	CNRQs, Quantitative reverse transcription PCR	RT-qPCR		Hermann, Bernd Timo	Quantitative reverse transcription polymerase chain reaction (qRT-PCR)	Lipoprotein-Lipase
39	CNRQs, Quantitative reverse transcription PCR	RT-qPCR		Hermann, Bernd Timo	Quantitative reverse transcription polymerase chain reaction (qRT-PCR)	Lysocyme C
40	CNRQs, Quantitative reverse transcription PCR	RT-qPCR		Hermann, Bernd Timo	Quantitative reverse transcription polymerase chain reaction (qRT-PCR)	Natural resistance associated macrophage protein
41	CNRQs, Quantitative reverse transcription PCR	RT-qPCR		Hermann, Bernd Timo	Quantitative reverse transcription polymerase chain reaction (qRT-PCR)	Protein Phosphatase 1 catalytic subunit beta
42	CNRQs, Quantitative reverse transcription PCR	RT-qPCR		Hermann, Bernd Timo	Quantitative reverse transcription polymerase chain reaction (qRT-PCR)	Peroxiredoxin 1
43	CNRQs, Quantitative reverse transcription PCR	RT-qPCR		Hermann, Bernd Timo	Quantitative reverse transcription polymerase chain reaction (qRT-PCR)	Signal transductor and activator of transcription 2
44	CNRQs, Quantitative reverse transcription PCR	RT-qPCR		Hermann, Bernd Timo	Quantitative reverse transcription polymerase chain reaction (qRT-PCR)	Transferrin
45	CNRQs, Quantitative reverse transcription PCR	RT-qPCR		Hermann, Bernd Timo	Quantitative reverse transcription polymerase chain reaction (qRT-PCR)	Transferrin receptor
46	CNRQs, Quantitative reverse transcription PCR	RT-qPCR		Hermann, Bernd Timo	Quantitative reverse transcription polymerase chain reaction (qRT-PCR)	Toll-like receptor 3
47	CNRQs, Quantitative reverse transcription PCR	RT-qPCR		Hermann, Bernd Timo	Quantitative reverse transcription polymerase chain reaction (qRT-PCR)	Tumor necrosis factor alpha
48	Gill, hypertrophied chloride cells	Gill HCC	%	Hermann, Bernd Timo	Microscopy
49	Gill, hyperplasia on basis of primary filament	Gill HbpF	%	Hermann, Bernd Timo	Microscopy
50	Gill, not affected	Gill NA	%	Hermann, Bernd Timo	Microscopy
51	Gill, hypertrophy of secondary lamellae	Gill HoSL	%	Hermann, Bernd Timo	Microscopy
52	Gill, hyperplasia on distal part of secondary lamellae	Gill HodPosL	%	Hermann, Bernd Timo	Microscopy
53	Gill, general hyperplasia	Gill GH	%	Hermann, Bernd Timo	Microscopy
54	Gill, lamellar clubbing	Gill LC	%	Hermann, Bernd Timo	Microscopy
55	Salinity	Sal		Hermann, Bernd Timo
56	Temperature, water	Temp	°C	Hermann, Bernd Timo
57	Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)	pCO2water_SST_wet	µatm	Hermann, Bernd Timo
58	Partial pressure of carbon dioxide, standard deviation	pCO2 std dev	±	Hermann, Bernd Timo
59	pH	pH		Hermann, Bernd Timo		NBS scale
60	pH, standard deviation	pH std dev	±	Hermann, Bernd Timo		NBS scale
61	Alkalinity, total	AT	µmol/kg	Hermann, Bernd Timo
62	Alkalinity, total, standard deviation	AT std dev	±	Hermann, Bernd Timo
63	Carbonate system computation flag	CSC flag		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
64	pH	pH		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	total scale
65	Carbon dioxide	CO2	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
66	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)
67	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)
68	Bicarbonate ion	[HCO3]-	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
69	Carbonate ion	[CO3]2-	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
70	Carbon, inorganic, dissolved	DIC	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
71	Aragonite saturation state	Omega Arg		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
72	Calcite saturation state	Omega Cal		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)

License:

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

Status:

Curation Level: Enhanced curation (CurationLevelC)

Size:

4447 data points

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