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Carreiro-Silva, Marina; Martins, Ines; Raimundo, Joana; Caetano, Miguel; Bettencourt, Raul; Cerqueira, Teresa; Colaço, Ana (2022): Gene expression by the cold-water octocoral Dentomuricea aff. meteor during an ex-situ experiment testing the effects of mining-generated sediment plumes [dataset]. PANGAEA, https://doi.org/10.1594/PANGAEA.948413, In: Carreiro-Silva, M et al. (2022): Results of an ex-situ experiment testing the effects of mining-generated sediment plumes on the cold-water octocoral Dentomuricea aff. meteor in the Azores [dataset bundled publication]. PANGAEA, https://doi.org/10.1594/PANGAEA.948414

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Abstract:
We report the results of an aquaria-based experiment testing the effects of suspended particles generated during potential mining activities, on a common habitat-building coral species in the Azores, Dentomuricea aff. meteor. Coral fragments were maintained in 10-L aquaria and exposed to three experimental treatments for a period of four weeks at the DeepSeaLab aquaria facilities (Okeanos-University of the Azores): (1) control conditions (no added sediments); (2) suspended polymetallic sulphide (PMS) particles; (3) suspended quartz particles. Gene expression profiles in D. aff. meteor were used to evaluate the physiological pathways involved in the response to exposure to PMS and quartz particles. Coral fragments were collected from each treatment at times 0, 3, and 13 days and for the control and quartz treatments also at time 27 days. The study targeted genes involved in cellular stress and antioxidant reaction system (heat shock protein, superoxide dismutase, ferritin), cell structure/integrity (α-carbonic anhydrase, receptor-type protein tyrosine phosphatase) and immune responses (toll-like receptor, lysozyme, rel homology domain, ferritin).
Keyword(s):
Cnidaria; enzyme activity; experiment; gene expression; metabolism; metal bioaccumulation; North Atlantic; octocorals
Related to:
Carreiro-Silva, Marina; Martins, Ines; Riou, Virginie; Raimundo, Joana; Caetano, Miguel; Bettencourt, Raul; Rakka, Maria; Cerqueira, Teresa; Godinho, Antonio; Morato, Telmo; Colaço, Ana (2022): Mechanical and toxicological effects of deep-sea mining sediment plumes on a habitat-forming cold-water octocoral. Frontiers in Marine Science, 9, 915650, https://doi.org/10.3389/fmars.2022.915650
Funding:
Fundação para a Ciência e Tecnologia (FCT), grant/award no. Mining2/0005/2017: Mining Impact 2
Horizon 2020 (H2020), grant/award no. 678760: A Trans-Atlantic assessment and deep-water ecosystem-based spatial management plan for Europe
Horizon 2020 (H2020), grant/award no. 818123: Integrated Assessment of Atlantic Marine Ecosystems in Space and Time
Seventh Framework Programme (FP7), grant/award no. 603418: Managing Impacts of Deep-seA reSource exploitation
Coverage:
Latitude: 38.539689 * Longitude: -29.039155
Date/Time Start: 2014-08-08T00:00:00 * Date/Time End: 2014-08-08T00:00:00
Minimum Elevation: -210.0 m * Maximum Elevation: -185.0 m
Event(s):
Sampling_Azores_Cold_Water_Octocoral * Latitude: 38.539689 * Longitude: -29.039155 * Date/Time: 2014-08-08T00:00:00 * Elevation Start: -185.0 m * Elevation End: -210.0 m * Location: Condor Seamounts * Comment: Sampling location of octoral specimens, Dentomuricea aff. meteor, studied in ex-situ aquaria experiments at the DeepSeaLab aquaria facilities of the Okeanos Institute, University of the Azores.
Comment:
Gene expression profiles in D. aff. meteor exposed to the different treatments
HKG: House Keeping Genes (18S and β-actin)
RHD: rel homology domain
TLR: toll-like receptor
HSP70: heat shock protein
RP Tyr-PH: receptor-type protein tyrosine phosphatase
SOD: superoxide dismutase
Carb Anhy: α-carbonic anhydrase
Ct = cycle threshold (nº of cycles in an RT-PCR required for the signal to exceed the background level)
Relative gene expression of the gene = Relative quantity gene / Geometric mean of the relative quantities of each housekeeping gene (=RQ gene/Geomean RQ HKGs)
Relative quantity (RQ) = (efficiency of the gene)^ΔCT
Parameter(s):
#NameShort NameUnitPrincipal InvestigatorMethod/DeviceComment
Gene nameGeneCarreiro-Silva, Marina
Specimen identificationSpec IDCarreiro-Silva, MarinaCoral colony
Experimental treatmentExp treatCarreiro-Silva, Marina
Experiment durationExp durationdaysCarreiro-Silva, Marina
CyclesCycles#Bettencourt, RaulReal-Time PCR, CFX Connect™ Real-Time PCR Detection System (BioRad)Cycle threshold CT
Gene expression, fold change, relativeGene expressionBettencourt, RaulReal-Time PCR, CFX Connect™ Real-Time PCR Detection System (BioRad)
Gene expression, fold change, relative, standard errorGene expression std e±Bettencourt, RaulReal-Time PCR, CFX Connect™ Real-Time PCR Detection System (BioRad)
Status:
Curation Level: Enhanced curation (CurationLevelC) * Processing Level: PANGAEA data processing level 3 (ProcLevel3)
Size:
2488 data points

Data

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


Gene

Spec ID

Exp treat

Exp duration [days]

Cycles [#]

Gene expression

Gene expression std e [±]
18S (HKG)5Control316.20
18S (HKG)10Control314.02
18S (HKG)11Control317.06
18S (HKG)12Control310.58
18S (HKG)13Control315.63
18S (HKG)14Control39.22
B-Actin (HKG)5Control313.94
B-Actin (HKG)10Control315.39
B-Actin (HKG)11Control315.39
B-Actin (HKG)12Control316.55
B-Actin (HKG)13Control316.89
B-Actin (HKG)14Control38.59
Lysozyme5Control335.090.0010290660.0003
Lysozyme10Control333.30
Lysozyme11Control333.50
Lysozyme12Control334.01
Lysozyme13Control332.14
Lysozyme14Control332.82
RHD5Control331.440.4808906360.0953
RHD10Control330.14
RHD11Control330.86
RHD12Control330.89
RHD13Control330.43
RHD14Control330.02
TLR5Control330.930.0098564370.0022
TLR10Control329.36
TLR11Control329.46
TLR12Control328.98
TLR13Control328.82
TLR14Control328.47
HSP 705Control330.710.0204905020.0038
HSP 7010Control329.59
HSP 7011Control329.73
HSP 7012Control329.39
HSP 7013Control328.91
HSP 7014Control329.69
RP Tyr-PH5Control327.720.0282761350.0055
RP Tyr-PH10Control326.34
RP Tyr-PH11Control326.95
RP Tyr-PH12Control327.06
RP Tyr-PH13Control325.40
RP Tyr-PH14Control327.01
SOD5Control328.900.0267695590.0048
SOD10Control328.24
SOD11Control328.78
SOD12Control329.74
SOD13Control328.86
SOD14Control329.89
Ferritin5Control330.490.0306149880.0069
Ferritin10Control329.32
Ferritin11Control329.77
Ferritin12Control329.85
Ferritin13Control328.58
Ferritin14Control329.91
Carb Anhy5Control330.900.0298507760.0061
Carb Anhy10Control329.38
Carb Anhy11Control329.10
Carb Anhy12Control328.75
Carb Anhy13Control329.05
Carb Anhy14Control327.71
18S (HKG)5Quartz315.99
18S (HKG)10Quartz315.23
18S (HKG)11Quartz312.17
18S (HKG)12Quartz312.31
18S (HKG)13Quartz316.70
18S (HKG)14Quartz312.55
B-Actin (HKG)5Quartz318.78
B-Actin (HKG)10Quartz318.54
B-Actin (HKG)11Quartz317.37
B-Actin (HKG)12Quartz318.56
B-Actin (HKG)13Quartz317.03
B-Actin (HKG)14Quartz316.23
Lysozyme5Quartz329.730.0500000000.0100
Lysozyme10Quartz329.35
Lysozyme11Quartz330.08
Lysozyme12Quartz330.21
Lysozyme13Quartz331.70
Lysozyme14Quartz333.35
RHD5Quartz332.870.4700000000.0700
RHD10Quartz331.49
RHD11Quartz333.31
RHD12Quartz332.31
RHD13Quartz333.49
RHD14Quartz333.35
TLR5Quartz329.080.0400000000.0100
TLR10Quartz328.18
TLR11Quartz328.41
TLR12Quartz329.52
TLR13Quartz329.92
TLR14Quartz331.82
HSP 705Quartz329.370.3900000000.0600
HSP 7010Quartz328.02
HSP 7011Quartz328.51
HSP 7012Quartz328.63
HSP 7013Quartz329.40
HSP 7014Quartz326.64
RP Tyr-PH5Quartz325.080.6600000000.1000
RP Tyr-PH10Quartz324.03
RP Tyr-PH11Quartz325.18
RP Tyr-PH12Quartz324.88
RP Tyr-PH13Quartz325.52
RP Tyr-PH14Quartz326.64
SOD5Quartz325.900.6400000000.1600
SOD10Quartz325.88
SOD11Quartz327.32
SOD12Quartz327.56
SOD13Quartz330.02
SOD14Quartz330.07
Ferritin5Quartz328.110.2000000000.0400
Ferritin10Quartz327.62
Ferritin11Quartz329.24
Ferritin12Quartz327.83
Ferritin13Quartz329.34
Ferritin14Quartz328.87
Carb Anhy5Quartz328.790.1300000000.0200
Carb Anhy10Quartz328.41
Carb Anhy11Quartz327.83
Carb Anhy12Quartz327.63
Carb Anhy13Quartz329.08
Carb Anhy14Quartz328.87
18S (HKG)5PMS316.81
18S (HKG)10PMS313.37
18S (HKG)11PMS314.13
18S (HKG)12PMS313.79
18S (HKG)13PMS312.30
18S (HKG)14PMS312.08
B-Actin (HKG)5PMS316.98
B-Actin (HKG)10PMS317.22
B-Actin (HKG)11PMS318.23
B-Actin (HKG)12PMS317.71
B-Actin (HKG)13PMS319.41
B-Actin (HKG)14PMS315.85
Lysozyme5PMS331.800.0167449180.0037
Lysozyme10PMS331.48
Lysozyme11PMS332.01
Lysozyme12PMS332.00
Lysozyme13PMS329.52
Lysozyme14PMS333.59
RHD5PMS334.690.1583243690.0239
RHD10PMS333.25
RHD11PMS334.63
RHD12PMS335.23
RHD13PMS332.32
RHD14PMS333.59
TLR5PMS330.890.0253442920.0063
TLR10PMS329.51
TLR11PMS330.26
TLR12PMS331.83
TLR13PMS326.17
TLR14PMS329.58
HSP 705PMS331.110.0716078290.0143
HSP 7010PMS330.34
HSP 7011PMS330.36
HSP 7012PMS331.38
HSP 7013PMS328.23
HSP 7014PMS326.77
RP Tyr-PH5PMS328.160.0552898990.0092
RP Tyr-PH10PMS328.79
RP Tyr-PH11PMS328.09
RP Tyr-PH12PMS328.55
RP Tyr-PH13PMS325.25
RP Tyr-PH14PMS326.77
SOD5PMS328.740.0815120750.0105
SOD10PMS329.56
SOD11PMS328.80
SOD12PMS329.96
SOD13PMS328.05
SOD14PMS330.42
Ferritin5PMS330.500.0699120480.0140
Ferritin10PMS331.44
Ferritin11PMS330.13
Ferritin12PMS329.78
Ferritin13PMS328.81
Ferritin14PMS328.66
Carb Anhy5PMS330.130.0790376720.0125
Carb Anhy10PMS330.23
Carb Anhy11PMS329.35
Carb Anhy12PMS329.81
Carb Anhy13PMS327.12
Carb Anhy14PMS328.66
18S (HKG)5Control1315.07
18S (HKG)10Control1314.30
18S (HKG)11Control1314.04
18S (HKG)12Control1311.52
18S (HKG)13Control1316.21
18S (HKG)14Control139.57
B-Actin (HKG)5Control1318.38
B-Actin (HKG)10Control1317.83
B-Actin (HKG)11Control1316.20
B-Actin (HKG)12Control1316.29
B-Actin (HKG)13Control1317.54
B-Actin (HKG)14Control1316.21
Lysozyme5Control1331.330.0992830740.0277
Lysozyme10Control1326.87
Lysozyme11Control1331.34
Lysozyme12Control1328.49
Lysozyme13Control1329.98
Lysozyme14Control1327.97
RHD5Control1334.010.2811649600.0549
RHD10Control1334.35
RHD11Control1333.45
RHD12Control1331.37
RHD13Control1332.16
RHD14Control1330.62
TLR5Control1331.170.0247530280.0059
TLR10Control1330.70
TLR11Control1330.27
TLR12Control1326.98
TLR13Control1329.20
TLR14Control1327.60
HSP 705Control1331.350.0987391710.0238
HSP 7010Control1331.37
HSP 7011Control1330.37
HSP 7012Control1326.83
HSP 7013Control1328.17
HSP 7014Control1327.10
RP Tyr-PH5Control1328.440.1781603920.0411
RP Tyr-PH10Control1326.57
RP Tyr-PH11Control1327.52
RP Tyr-PH12Control1324.01
RP Tyr-PH13Control1325.07
RP Tyr-PH14Control1323.76
SOD5Control1326.260.9350618570.1285
SOD10Control1326.71
SOD11Control1325.90
SOD12Control1325.62
SOD13Control1326.73
SOD14Control1327.04
Ferritin5Control1328.740.3634297220.0737
Ferritin10Control1328.77
Ferritin11Control1328.26
Ferritin12Control1326.93
Ferritin13Control1327.86
Ferritin14Control1327.09
Carb Anhy5Control1324.570.9686446930.1519
Carb Anhy10Control1326.19
Carb Anhy11Control1326.29
Carb Anhy12Control1325.05
Carb Anhy13Control1326.51
Carb Anhy14Control1326.27
18S (HKG)5Quartz1316.34
18S (HKG)10Quartz1311.44
18S (HKG)11Quartz1316.45
18S (HKG)12Quartz1311.20
18S (HKG)13Quartz1314.54
18S (HKG)14Quartz139.91
B-Actin (HKG)5Quartz1318.33
B-Actin (HKG)10Quartz1317.08
B-Actin (HKG)11Quartz1317.61
B-Actin (HKG)12Quartz1317.59
B-Actin (HKG)13Quartz1316.44
B-Actin (HKG)14Quartz1315.95
Lysozyme5Quartz1331.280.0308858890.0065
Lysozyme10Quartz1329.98
Lysozyme11Quartz1331.33
Lysozyme12Quartz1330.28
Lysozyme13Quartz1329.29
Lysozyme14Quartz1331.53
RHD5Quartz1334.470.1849619970.0346
RHD10Quartz1333.43
RHD11Quartz1334.48
RHD12Quartz1333.37
RHD13Quartz1331.95
RHD14Quartz1331.53
TLR5Quartz1330.540.0214765750.0038
TLR10Quartz1328.79
TLR11Quartz1330.18
TLR12Quartz1328.84
TLR13Quartz1328.86
TLR14Quartz1329.51
HSP 705Quartz1330.610.0632769370.0147
HSP 7010Quartz1328.59
HSP 7011Quartz1330.95
HSP 7012Quartz1329.26
HSP 7013Quartz1328.38
HSP 7014Quartz1326.10
RP Tyr-PH5Quartz1328.230.0683050300.0142
RP Tyr-PH10Quartz1325.24
RP Tyr-PH11Quartz1327.60
RP Tyr-PH12Quartz1326.60
RP Tyr-PH13Quartz1324.69
RP Tyr-PH14Quartz1326.10
SOD5Quartz1327.850.3104220910.0538
SOD10Quartz1326.24
SOD11Quartz1326.27
SOD12Quartz1326.29
SOD13Quartz1327.40
SOD14Quartz1327.74
Ferritin5Quartz1329.970.2027712090.0505
Ferritin10Quartz1328.70
Ferritin11Quartz1328.63
Ferritin12Quartz1327.40
Ferritin13Quartz1326.99
Ferritin14Quartz1326.46
Carb Anhy5Quartz1328.030.4465781460.0836
Carb Anhy10Quartz1325.39
Carb Anhy11Quartz1326.07
Carb Anhy12Quartz1325.83
Carb Anhy13Quartz1325.23
Carb Anhy14Quartz1326.46
18S (HKG)5PMS1313.54
18S (HKG)10PMS1311.65
18S (HKG)11PMS1314.02
18S (HKG)12PMS1313.80
18S (HKG)13PMS1315.07
18S (HKG)14PMS138.32
B-Actin (HKG)5PMS1316.95
B-Actin (HKG)10PMS1315.21
B-Actin (HKG)11PMS1316.49
B-Actin (HKG)12PMS1315.60
B-Actin (HKG)13PMS1316.34
B-Actin (HKG)14PMS1315.91
Lysozyme5PMS1331.020.0104941790.0019
Lysozyme10PMS1331.05
Lysozyme11PMS1331.50
Lysozyme12PMS1330.60
Lysozyme13PMS1330.13
Lysozyme14PMS1331.83
RHD5PMS1334.430.0832637950.0138
RHD10PMS1333.54
RHD11PMS1334.37
RHD12PMS1333.58
RHD13PMS1332.12
RHD14PMS1331.83
TLR5PMS1330.420.0082712000.0013
TLR10PMS1329.08
TLR11PMS1330.33
TLR12PMS1329.17
TLR13PMS1330.43
TLR14PMS1328.98
HSP 705PMS1330.980.0387055900.0097
HSP 7010PMS1329.79
HSP 7011PMS1330.73
HSP 7012PMS1329.35
HSP 7013PMS1328.50
HSP 7014PMS1325.01
RP Tyr-PH5PMS1328.120.0291974830.0058
RP Tyr-PH10PMS1327.53
RP Tyr-PH11PMS1328.48
RP Tyr-PH12PMS1327.58
RP Tyr-PH13PMS1325.28
RP Tyr-PH14PMS1325.01
SOD5PMS1328.610.1502047670.0237
SOD10PMS1326.24
SOD11PMS1327.10
SOD12PMS1327.54
SOD13PMS1327.69
SOD14PMS1326.62
Ferritin5PMS1330.580.1082310610.0305
Ferritin10PMS1328.44
Ferritin11PMS1329.50
Ferritin12PMS1328.49
Ferritin13PMS1328.39
Ferritin14PMS1325.27
Carb Anhy5PMS1329.850.1776135910.0383
Carb Anhy10PMS1326.25
Carb Anhy11PMS1327.06
Carb Anhy12PMS1327.13
Carb Anhy13PMS1326.75
Carb Anhy14PMS1325.27
18S (HKG)5Control27
18S (HKG)10Control27
18S (HKG)11Control2720.82
18S (HKG)12Control27
18S (HKG)13Control2718.40
18S (HKG)14Control27
B-Actin (HKG)5Control27
B-Actin (HKG)10Control27
B-Actin (HKG)11Control2717.33
B-Actin (HKG)12Control27
B-Actin (HKG)13Control2717.84
B-Actin (HKG)14Control27
Lysozyme5Control270.3069816190.1403
Lysozyme10Control27
Lysozyme11Control2732.96
Lysozyme12Control27
Lysozyme13Control2730.38
Lysozyme14Control27
RHD5Control271.6302458920.6175
RHD10Control27
RHD11Control2736.11
RHD12Control27
RHD13Control2733.26
RHD14Control27
TLR5Control270.1821355690.0742
TLR10Control27
TLR11Control2731.80
TLR12Control27
TLR13Control2729.25
TLR14Control27
HSP 705Control270.7310674260.2563
HSP 7010Control27
HSP 7011Control2731.60
HSP 7012Control27
HSP 7013Control2729.07
HSP 7014Control27
RP Tyr-PH5Control271.3379754860.6395
RP Tyr-PH10Control27
RP Tyr-PH11Control2729.14
RP Tyr-PH12Control27
RP Tyr-PH13Control2725.46
RP Tyr-PH14Control27
SOD5Control270.8396448690.4024
SOD10Control27
SOD11Control2731.57
SOD12Control27
SOD13Control2728.43
SOD14Control27
Ferritin5Control271.5130041490.5803
Ferritin10Control27
Ferritin11Control2731.23
Ferritin12Control27
Ferritin13Control2729.50
Ferritin14Control27
Carb Anhy5Control270.5295648690.2300
Carb Anhy10Control27
Carb Anhy11Control2732.91
Carb Anhy12Control27
Carb Anhy13Control2729.81
Carb Anhy14Control27
18S (HKG)5Quartz2721.03
18S (HKG)10Quartz2716.86
18S (HKG)11Quartz2717.28
18S (HKG)12Quartz2718.86
18S (HKG)13Quartz2719.02
18S (HKG)14Quartz2714.46
B-Actin (HKG)5Quartz2718.15
B-Actin (HKG)10Quartz2718.91
B-Actin (HKG)11Quartz2717.05
B-Actin (HKG)12Quartz2717.32
B-Actin (HKG)13Quartz2715.79
B-Actin (HKG)14Quartz2717.78
Lysozyme5Quartz2732.630.8565648760.2799
Lysozyme10Quartz2727.85
Lysozyme11Quartz2730.27
Lysozyme12Quartz2729.06
Lysozyme13Quartz2731.28
Lysozyme14Quartz2726.17
RHD5Quartz2735.842.4624007710.6551
RHD10Quartz2731.35
RHD11Quartz2734.17
RHD12Quartz2731.72
RHD13Quartz2734.87
RHD14Quartz2729.48
TLR5Quartz2733.010.4571768070.2099
TLR10Quartz2726.55
TLR11Quartz2730.19
TLR12Quartz2727.89
TLR13Quartz2730.95
TLR14Quartz2725.33
HSP 705Quartz2732.881.6279826370.6841
HSP 7010Quartz2726.26
HSP 7011Quartz2729.72
HSP 7012Quartz2728.30
HSP 7013Quartz2730.05
HSP 7014Quartz2724.96
RP Tyr-PH5Quartz2730.091.3141127830.5537
RP Tyr-PH10Quartz2724.38
RP Tyr-PH11Quartz2727.22
RP Tyr-PH12Quartz2724.86
RP Tyr-PH13Quartz2728.19
RP Tyr-PH14Quartz2723.03
SOD5Quartz2730.691.5235141600.5897
SOD10Quartz2727.00
SOD11Quartz2728.12
SOD12Quartz2727.63
SOD13Quartz2730.58
SOD14Quartz2726.76
Ferritin5Quartz2731.362.2398568400.9770
Ferritin10Quartz2727.49
Ferritin11Quartz2729.24
Ferritin12Quartz2727.71
Ferritin13Quartz2729.89
Ferritin14Quartz2725.12
Carb Anhy5Quartz2731.630.8208234860.3190
Carb Anhy10Quartz2728.01
Carb Anhy11Quartz2730.08
Carb Anhy12Quartz2727.60
Carb Anhy13Quartz2731.35
Carb Anhy14Quartz2727.22