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Dineshram, R; Wong, Kevin K W; Shu, Xiao; Yu, Ziniu; Qian, Pei Yuan; Thiyagarajan, Vengatesen (2012): Analysis of Pacific oyster larval proteome and its response to high-CO2 [dataset]. PANGAEA, https://doi.org/10.1594/PANGAEA.823757, Supplement to: Dineshram, R et al. (2012): Analysis of Pacific oyster larval proteome and its response to high-CO2. Marine Pollution Bulletin, 64(10), 2160-2167, https://doi.org/10.1016/j.marpolbul.2012.07.043

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Abstract:
Most calcifying organisms show depressed metabolic, growth and calcification rates as symptoms to high-CO(2) due to ocean acidification (OA) process. Analysis of the global expression pattern of proteins (proteome analysis) represents a powerful tool to examine these physiological symptoms at molecular level, but its applications are inadequate. To address this knowledge gap, 2-DE coupled with mass spectrophotometer was used to compare the global protein expression pattern of oyster larvae exposed to ambient and to high-CO(2). Exposure to OA resulted in marked reduction of global protein expression with a decrease or loss of 71 proteins (18% of the expressed proteins in control), indicating a wide-spread depression of metabolic genes expression in larvae reared under OA. This is, to our knowledge, the first proteome analysis that provides insights into the link between physiological suppression and protein down-regulation under OA in oyster larvae.
Keyword(s):
Animalia; Coast and continental shelf; Containers and aquaria (20-1000 L or < 1 m**2); Crassostrea gigas; Gene expression (incl. proteomics); Growth/Morphology; Laboratory experiment; Mollusca; North Pacific; Pelagos; Single species; Tropical; Zooplankton
Further details:
Lavigne, Héloïse; Gattuso, Jean-Pierre (2011): seacarb: seawater carbonate chemistry with R. R package version 2.4. https://cran.r-project.org/package=seacarb
Comment:
In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Lavigne and Gattuso, 2011) 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 2014-02-20.
Parameter(s):
#NameShort NameUnitPrincipal InvestigatorMethod/DeviceComment
SpeciesSpeciesThiyagarajan, Vengatesen
IdentificationIDThiyagarajan, Vengatesen
Duration, number of daysDurationdaysThiyagarajan, Vengatesendays after fertilization
ReplicateReplThiyagarajan, Vengatesen
TreatmentTreatThiyagarajan, Vengatesen
Shell lengthShell lmmThiyagarajan, Vengatesen
Protein nameProteinThiyagarajan, Vengatesen
Spot intensity, relativeSpot intenThiyagarajan, Vengatesen
SalinitySalThiyagarajan, Vengatesen
10 Temperature, waterTemp°CThiyagarajan, Vengatesen
11 Alkalinity, totalATµmol/kgThiyagarajan, Vengatesen
12 pHpHThiyagarajan, VengatesenNBS scale
13 Carbon, inorganic, dissolvedDICµmol/kgThiyagarajan, VengatesenCalculated using CO2SYS
14 Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)pCO2water_SST_wetµatmThiyagarajan, VengatesenCalculated using CO2SYS
15 Carbon dioxideCO2µmol/kgThiyagarajan, VengatesenCalculated using CO2SYS
16 Bicarbonate ion[HCO3]-µmol/kgThiyagarajan, VengatesenCalculated using CO2SYS
17 Carbonate ion[CO3]2-µmol/kgThiyagarajan, VengatesenCalculated using CO2SYS
18 Calcite saturation stateOmega CalThiyagarajan, VengatesenCalculated using CO2SYS
19 Aragonite saturation stateOmega ArgThiyagarajan, VengatesenCalculated using CO2SYS
20 Carbonate system computation flagCSC flagYang, YanCalculated using seacarb after Nisumaa et al. (2010)
21 pHpHYang, YanCalculated using seacarb after Nisumaa et al. (2010)total scale
22 Carbon dioxideCO2µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
23 Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)pCO2water_SST_wetµatmYang, YanCalculated using seacarb after Nisumaa et al. (2010)
24 Fugacity of carbon dioxide (water) at sea surface temperature (wet air)fCO2water_SST_wetµatmYang, YanCalculated using seacarb after Nisumaa et al. (2010)
25 Bicarbonate ion[HCO3]-µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
26 Carbonate ion[CO3]2-µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
27 Carbon, inorganic, dissolvedDICµmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
28 Aragonite saturation stateOmega ArgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
29 Calcite saturation stateOmega CalYang, YanCalculated using seacarb after Nisumaa et al. (2010)
Status:
Curation Level: Enhanced curation (CurationLevelC)
Size:
1861 data points

Data

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


Species

ID

Duration [days]
(days after fertilization)

Repl

Treat

Shell l [mm]

Protein

Spot inten

Sal
10 
Temp [°C]
11 
AT [µmol/kg]
12 
pH
(NBS scale)
13 
DIC [µmol/kg]
(Calculated using CO2SYS)
14 
pCO2water_SST_wet [µatm]
(Calculated using CO2SYS)
15 
CO2 [µmol/kg]
(Calculated using CO2SYS)
16 
[HCO3]- [µmol/kg]
(Calculated using CO2SYS)
17 
[CO3]2- [µmol/kg]
(Calculated using CO2SYS)
18 
Omega Cal
(Calculated using CO2SYS)
19 
Omega Arg
(Calculated using CO2SYS)
20 
CSC flag
(Calculated using seacarb afte...)
21 
pH
(total scale, Calculated using...)
22 
CO2 [µmol/kg]
(Calculated using seacarb afte...)
23 
pCO2water_SST_wet [µatm]
(Calculated using seacarb afte...)
24 
fCO2water_SST_wet [µatm]
(Calculated using seacarb afte...)
25 
[HCO3]- [µmol/kg]
(Calculated using seacarb afte...)
26 
[CO3]2- [µmol/kg]
(Calculated using seacarb afte...)
27 
DIC [µmol/kg]
(Calculated using seacarb afte...)
28 
Omega Arg
(Calculated using seacarb afte...)
29 
Omega Cal
(Calculated using seacarb afte...)
Crassostrea gigas (Mollusk)Figure 14Treatment R1pH=7.50.07846252918947.481918.192624.9570.891814.4932.820.870.56267.3361.92290.42283.51804.137.11903.00.630.98
Crassostrea gigas (Mollusk)Figure 14Treatment R2pH=7.50.08301252915707.471576.191926.1052.011493.8630.320.800.52267.3252.41941.41935.51494.630.01577.00.510.79
Crassostrea gigas (Mollusk)Figure 14Treatment R3pH=7.50.08660252926
Crassostrea gigas (Mollusk)Figure 16Treatment R1pH=7.50.08805252918947.481918.192624.9570.891814.4932.820.870.56267.3361.92290.42283.51804.137.11903.00.630.98
Crassostrea gigas (Mollusk)Figure 16Treatment R2pH=7.50.08730252915707.471576.191926.1052.011493.8630.320.800.52267.3252.41941.41935.51494.630.01577.00.510.79
Crassostrea gigas (Mollusk)Figure 16Treatment R3pH=7.50.09411252926
Crassostrea gigas (Mollusk)Figure 14Control R1pH=80.08537252919457.931799.68634.6317.141667.84114.703.031.96267.7820.8769.0766.71706.398.71825.81.682.61
Crassostrea gigas (Mollusk)Figure 14Control R2pH=80.08471252920037.901854.70654.0317.661718.83118.203.122.02267.7523.1856.1853.51772.795.71891.61.632.53
Crassostrea gigas (Mollusk)Figure 14Control R3pH=80.08381252919827.921834.30646.8417.471699.93116.903.091.99267.7721.7804.2801.81743.898.61864.21.682.60
Crassostrea gigas (Mollusk)Figure 16Control R1pH=80.09774252919457.931799.68634.6317.141667.84114.703.031.96267.7820.8769.0766.71706.398.71825.81.682.61
Crassostrea gigas (Mollusk)Figure 16Control R2pH=80.09522252920037.901854.70654.0317.661718.83118.203.122.02267.7523.1856.1853.51772.795.71891.61.632.53
Crassostrea gigas (Mollusk)Figure 16Control R3pH=80.10083252919827.921834.30646.8417.471699.93116.903.091.99267.7721.7804.2801.81743.898.61864.21.682.60
Crassostrea gigas (Mollusk)Figure 4Control R1pH=8Calmodulin7050.2252919457.931799.68634.6317.141667.84114.703.031.96267.7820.8769.0766.71706.398.71825.81.682.61
Crassostrea gigas (Mollusk)Figure 4Control R1pH=8Beta-tubulin7065.0252919457.931799.68634.6317.141667.84114.703.031.96267.7820.8769.0766.71706.398.71825.81.682.61
Crassostrea gigas (Mollusk)Figure 4Control R1pH=8Calmodulin4124.0252919457.931799.68634.6317.141667.84114.703.031.96267.7820.8769.0766.71706.398.71825.81.682.61
Crassostrea gigas (Mollusk)Figure 4Control R1pH=8Troponin C3421.3252919457.931799.68634.6317.141667.84114.703.031.96267.7820.8769.0766.71706.398.71825.81.682.61
Crassostrea gigas (Mollusk)Figure 4Control R1pH=8Cytochrome C oxidase3574.1252919457.931799.68634.6317.141667.84114.703.031.96267.7820.8769.0766.71706.398.71825.81.682.61
Crassostrea gigas (Mollusk)Figure 4Control R1pH=8Tektin881.9252919457.931799.68634.6317.141667.84114.703.031.96267.7820.8769.0766.71706.398.71825.81.682.61
Crassostrea gigas (Mollusk)Figure 4Control R1pH=8Serine/threonine-protein phosphatase1059.5252919457.931799.68634.6317.141667.84114.703.031.96267.7820.8769.0766.71706.398.71825.81.682.61
Crassostrea gigas (Mollusk)Figure 4Control R1pH=8annexin1583.7252919457.931799.68634.6317.141667.84114.703.031.96267.7820.8769.0766.71706.398.71825.81.682.61
Crassostrea gigas (Mollusk)Figure 4Control R1pH=8Nucleoside diphosphate kinase852.5252919457.931799.68634.6317.141667.84114.703.031.96267.7820.8769.0766.71706.398.71825.81.682.61
Crassostrea gigas (Mollusk)Figure 4Control R1pH=8Fascilin2761.1252919457.931799.68634.6317.141667.84114.703.031.96267.7820.8769.0766.71706.398.71825.81.682.61
Crassostrea gigas (Mollusk)Figure 4Control R1pH=8vacuolar H[+]-ATPase1193.2252919457.931799.68634.6317.141667.84114.703.031.96267.7820.8769.0766.71706.398.71825.81.682.61
Crassostrea gigas (Mollusk)Figure 4Control R2pH=8Calmodulin8862.9252920037.901854.70654.0317.661718.83118.203.122.02267.7523.1856.1853.51772.795.71891.61.632.53
Crassostrea gigas (Mollusk)Figure 4Control R2pH=8Beta-tubulin5824.7252920037.901854.70654.0317.661718.83118.203.122.02267.7523.1856.1853.51772.795.71891.61.632.53
Crassostrea gigas (Mollusk)Figure 4Control R2pH=8Calmodulin4370.8252920037.901854.70654.0317.661718.83118.203.122.02267.7523.1856.1853.51772.795.71891.61.632.53
Crassostrea gigas (Mollusk)Figure 4Control R2pH=8Troponin C1750.8252920037.901854.70654.0317.661718.83118.203.122.02267.7523.1856.1853.51772.795.71891.61.632.53
Crassostrea gigas (Mollusk)Figure 4Control R2pH=8Cytochrome C oxidase4298.7252920037.901854.70654.0317.661718.83118.203.122.02267.7523.1856.1853.51772.795.71891.61.632.53
Crassostrea gigas (Mollusk)Figure 4Control R2pH=8Tektin794.3252920037.901854.70654.0317.661718.83118.203.122.02267.7523.1856.1853.51772.795.71891.61.632.53
Crassostrea gigas (Mollusk)Figure 4Control R2pH=8Serine/threonine-protein phosphatase1707.4252920037.901854.70654.0317.661718.83118.203.122.02267.7523.1856.1853.51772.795.71891.61.632.53
Crassostrea gigas (Mollusk)Figure 4Control R2pH=8annexin2427.7252920037.901854.70654.0317.661718.83118.203.122.02267.7523.1856.1853.51772.795.71891.61.632.53
Crassostrea gigas (Mollusk)Figure 4Control R2pH=8Nucleoside diphosphate kinase1439.4252920037.901854.70654.0317.661718.83118.203.122.02267.7523.1856.1853.51772.795.71891.61.632.53
Crassostrea gigas (Mollusk)Figure 4Control R2pH=8Fascilin3932.0252920037.901854.70654.0317.661718.83118.203.122.02267.7523.1856.1853.51772.795.71891.61.632.53
Crassostrea gigas (Mollusk)Figure 4Control R2pH=8vacuolar H[+]-ATPase1599.2252920037.901854.70654.0317.661718.83118.203.122.02267.7523.1856.1853.51772.795.71891.61.632.53
Crassostrea gigas (Mollusk)Figure 4Control R3pH=8Calmodulin7928.8252919827.921834.30646.8417.471699.93116.903.091.99267.7721.7804.2801.81743.898.61864.21.682.60
Crassostrea gigas (Mollusk)Figure 4Control R3pH=8Beta-tubulin8521.3252919827.921834.30646.8417.471699.93116.903.091.99267.7721.7804.2801.81743.898.61864.21.682.60
Crassostrea gigas (Mollusk)Figure 4Control R3pH=8Calmodulin5441.9252919827.921834.30646.8417.471699.93116.903.091.99267.7721.7804.2801.81743.898.61864.21.682.60
Crassostrea gigas (Mollusk)Figure 4Control R3pH=8Troponin C2798.2252919827.921834.30646.8417.471699.93116.903.091.99267.7721.7804.2801.81743.898.61864.21.682.60
Crassostrea gigas (Mollusk)Figure 4Control R3pH=8Cytochrome C oxidase3004.4252919827.921834.30646.8417.471699.93116.903.091.99267.7721.7804.2801.81743.898.61864.21.682.60
Crassostrea gigas (Mollusk)Figure 4Control R3pH=8Tektin1701.9252919827.921834.30646.8417.471699.93116.903.091.99267.7721.7804.2801.81743.898.61864.21.682.60
Crassostrea gigas (Mollusk)Figure 4Control R3pH=8Serine/threonine-protein phosphatase1070.2252919827.921834.30646.8417.471699.93116.903.091.99267.7721.7804.2801.81743.898.61864.21.682.60
Crassostrea gigas (Mollusk)Figure 4Control R3pH=8annexin945.8252919827.921834.30646.8417.471699.93116.903.091.99267.7721.7804.2801.81743.898.61864.21.682.60
Crassostrea gigas (Mollusk)Figure 4Control R3pH=8Nucleoside diphosphate kinase714.8252919827.921834.30646.8417.471699.93116.903.091.99267.7721.7804.2801.81743.898.61864.21.682.60
Crassostrea gigas (Mollusk)Figure 4Control R3pH=8Fascilin4849.1252919827.921834.30646.8417.471699.93116.903.091.99267.7721.7804.2801.81743.898.61864.21.682.60
Crassostrea gigas (Mollusk)Figure 4Control R3pH=8vacuolar H[+]-ATPase875.4252919827.921834.30646.8417.471699.93116.903.091.99267.7721.7804.2801.81743.898.61864.21.682.60
Crassostrea gigas (Mollusk)Figure 4Treatment R1pH=7.5Calmodulin2425.3252918947.481918.192624.9570.891814.4932.820.870.56267.3361.92290.42283.51804.137.11903.00.630.98
Crassostrea gigas (Mollusk)Figure 4Treatment R1pH=7.5Beta-tubulin2083.0252918947.481918.192624.9570.891814.4932.820.870.56267.3361.92290.42283.51804.137.11903.00.630.98
Crassostrea gigas (Mollusk)Figure 4Treatment R1pH=7.5Calmodulin410.0252918947.481918.192624.9570.891814.4932.820.870.56267.3361.92290.42283.51804.137.11903.00.630.98
Crassostrea gigas (Mollusk)Figure 4Treatment R1pH=7.5Troponin C418.0252918947.481918.192624.9570.891814.4932.820.870.56267.3361.92290.42283.51804.137.11903.00.630.98
Crassostrea gigas (Mollusk)Figure 4Treatment R1pH=7.5Cytochrome C oxidase425.0252918947.481918.192624.9570.891814.4932.820.870.56267.3361.92290.42283.51804.137.11903.00.630.98
Crassostrea gigas (Mollusk)Figure 4Treatment R1pH=7.5Tektin471.6252918947.481918.192624.9570.891814.4932.820.870.56267.3361.92290.42283.51804.137.11903.00.630.98
Crassostrea gigas (Mollusk)Figure 4Treatment R1pH=7.5Serine/threonine-protein phosphatase415.0252918947.481918.192624.9570.891814.4932.820.870.56267.3361.92290.42283.51804.137.11903.00.630.98
Crassostrea gigas (Mollusk)Figure 4Treatment R1pH=7.5annexin4641.5252918947.481918.192624.9570.891814.4932.820.870.56267.3361.92290.42283.51804.137.11903.00.630.98
Crassostrea gigas (Mollusk)Figure 4Treatment R1pH=7.5Nucleoside diphosphate kinase2635.2252918947.481918.192624.9570.891814.4932.820.870.56267.3361.92290.42283.51804.137.11903.00.630.98
Crassostrea gigas (Mollusk)Figure 4Treatment R1pH=7.5Fascilin21598.0252918947.481918.192624.9570.891814.4932.820.870.56267.3361.92290.42283.51804.137.11903.00.630.98
Crassostrea gigas (Mollusk)Figure 4Treatment R1pH=7.5vacuolar H[+]-ATPase2890.8252918947.481918.192624.9570.891814.4932.820.870.56267.3361.92290.42283.51804.137.11903.00.630.98
Crassostrea gigas (Mollusk)Figure 4Treatment R2pH=7.5Calmodulin4665.6252915707.471576.191926.1052.011493.8630.320.800.52267.3252.41941.41935.51494.630.01577.00.510.79
Crassostrea gigas (Mollusk)Figure 4Treatment R2pH=7.5Beta-tubulin2750.1252915707.471576.191926.1052.011493.8630.320.800.52267.3252.41941.41935.51494.630.01577.00.510.79
Crassostrea gigas (Mollusk)Figure 4Treatment R2pH=7.5Calmodulin1021.7252915707.471576.191926.1052.011493.8630.320.800.52267.3252.41941.41935.51494.630.01577.00.510.79
Crassostrea gigas (Mollusk)Figure 4Treatment R2pH=7.5Troponin C816.0252915707.471576.191926.1052.011493.8630.320.800.52267.3252.41941.41935.51494.630.01577.00.510.79
Crassostrea gigas (Mollusk)Figure 4Treatment R2pH=7.5Cytochrome C oxidase577.1252915707.471576.191926.1052.011493.8630.320.800.52267.3252.41941.41935.51494.630.01577.00.510.79
Crassostrea gigas (Mollusk)Figure 4Treatment R2pH=7.5Tektin1294.6252915707.471576.191926.1052.011493.8630.320.800.52267.3252.41941.41935.51494.630.01577.00.510.79
Crassostrea gigas (Mollusk)Figure 4Treatment R2pH=7.5Serine/threonine-protein phosphatase510.0252915707.471576.191926.1052.011493.8630.320.800.52267.3252.41941.41935.51494.630.01577.00.510.79
Crassostrea gigas (Mollusk)Figure 4Treatment R2pH=7.5annexin4046.9252915707.471576.191926.1052.011493.8630.320.800.52267.3252.41941.41935.51494.630.01577.00.510.79
Crassostrea gigas (Mollusk)Figure 4Treatment R2pH=7.5Nucleoside diphosphate kinase2189.2252915707.471576.191926.1052.011493.8630.320.800.52267.3252.41941.41935.51494.630.01577.00.510.79
Crassostrea gigas (Mollusk)Figure 4Treatment R2pH=7.5Fascilin15283.5252915707.471576.191926.1052.011493.8630.320.800.52267.3252.41941.41935.51494.630.01577.00.510.79
Crassostrea gigas (Mollusk)Figure 4Treatment R2pH=7.5vacuolar H[+]-ATPase2422.1252915707.471576.191926.1052.011493.8630.320.800.52267.3252.41941.41935.51494.630.01577.00.510.79
Crassostrea gigas (Mollusk)Figure 4Treatment R3pH=7.5Calmodulin4879.72529
Crassostrea gigas (Mollusk)Figure 4Treatment R3pH=7.5Beta-tubulin1892.72529
Crassostrea gigas (Mollusk)Figure 4Treatment R3pH=7.5Calmodulin1321.02529
Crassostrea gigas (Mollusk)Figure 4Treatment R3pH=7.5Troponin C675.62529
Crassostrea gigas (Mollusk)Figure 4Treatment R3pH=7.5Cytochrome C oxidase1739.62529
Crassostrea gigas (Mollusk)Figure 4Treatment R3pH=7.5Tektin301.02529
Crassostrea gigas (Mollusk)Figure 4Treatment R3pH=7.5Serine/threonine-protein phosphatase367.02529
Crassostrea gigas (Mollusk)Figure 4Treatment R3pH=7.5annexin2592.02529
Crassostrea gigas (Mollusk)Figure 4Treatment R3pH=7.5Nucleoside diphosphate kinase2175.52529
Crassostrea gigas (Mollusk)Figure 4Treatment R3pH=7.5Fascilin15385.02529
Crassostrea gigas (Mollusk)Figure 4Treatment R3pH=7.5vacuolar H[+]-ATPase2688.32529