Seawater carbonate chemistry and gene expression stability of Hong Kong oyster (Crassostrea hongkongensis)
The increase of CO2 by anthropogenic activities leads to a decrease of pH in the ocean surface due to ocean acidification (OA) process. Generally, OA not only reduces the rate of calcification in marine environments but also affects various physiological activities, especially in calcifiers, includi...
Main Authors: | , , , , , , |
---|---|
Format: | Dataset |
Language: | English |
Published: |
PANGAEA
2022
|
Subjects: | |
Online Access: | https://doi.pangaea.de/10.1594/PANGAEA.945551 https://doi.org/10.1594/PANGAEA.945551 |
id |
ftpangaea:oai:pangaea.de:doi:10.1594/PANGAEA.945551 |
---|---|
record_format |
openpolar |
spelling |
ftpangaea:oai:pangaea.de:doi:10.1594/PANGAEA.945551 2023-05-15T17:51:06+02:00 Seawater carbonate chemistry and gene expression stability of Hong Kong oyster (Crassostrea hongkongensis) Dang, Xin Noor, Zohaib He, Yuanqiu Lim, Yong-Kian Zhang, Yang Yu, Ziniu Thiyagarajan, Vengatesen LATITUDE: 21.590000 * LONGITUDE: 108.980000 2022-06-21 text/tab-separated-values, 4590 data points https://doi.pangaea.de/10.1594/PANGAEA.945551 https://doi.org/10.1594/PANGAEA.945551 en eng PANGAEA Dang, Xin; Noor, Zohaib; He, Yuanqiu; Lim, Yong-Kian; Zhang, Yang; Yu, Ziniu; Thiyagarajan, Vengatesen (2022): Internal controls for quantitative RT-PCR analysis of gene expression in response to ocean acidification in edible oysters. Journal of Experimental Marine Biology and Ecology, 548, 151683, https://doi.org/10.1016/j.jembe.2021.151683 Gattuso, Jean-Pierre; Epitalon, Jean-Marie; Lavigne, Héloïse; Orr, James (2021): seacarb: seawater carbonate chemistry with R. R package version 3.2.16. https://cran.r-project.org/web/packages/seacarb/index.html https://doi.pangaea.de/10.1594/PANGAEA.945551 https://doi.org/10.1594/PANGAEA.945551 CC-BY-4.0: Creative Commons Attribution 4.0 International Access constraints: unrestricted info:eu-repo/semantics/openAccess CC-BY Alkalinity total Animalia Aragonite saturation state Beihai_OA Benthic animals Benthos Bicarbonate ion Calcite saturation state Calculated using seacarb after Nisumaa et al. (2010) Carbon inorganic dissolved Carbonate ion Carbonate system computation flag Carbon dioxide Coast and continental shelf Containers and aquaria (20-1000 L or < 1 m**2) EXP Experiment Fugacity of carbon dioxide (water) at sea surface temperature (wet air) Gene expression (incl. proteomics) Gene name Laboratory experiment Magallana hongkongensis Mollusca North Pacific OA-ICC Ocean Acidification International Coordination Centre Partial pressure of carbon dioxide (water) at sea surface temperature (wet air) pH Salinity Single species Species unique identification unique identification (Semantic URI) unique identification (URI) Stability Temperature water Treatment Tropical Type Dataset 2022 ftpangaea https://doi.org/10.1594/PANGAEA.945551 https://doi.org/10.1016/j.jembe.2021.151683 2023-01-20T09:16:08Z The increase of CO2 by anthropogenic activities leads to a decrease of pH in the ocean surface due to ocean acidification (OA) process. Generally, OA not only reduces the rate of calcification in marine environments but also affects various physiological activities, especially in calcifiers, including edible oysters. Quantitative real-time PCR (qRT-PCR) is often used to detect gene expression in response to OA, which relies on the stability of internal control. However, the appropriate internal controls for OA experiments remain scarce especially in the marine calcifiers. Hence, this study developed internal controls for qRT-PCR assays using the Hong Kong oyster (Crassostrea hongkongensis) as a model to reveal gene expression profile during development under OA. In this study, 17 housekeeping genes were selected as the possible candidate of the internal controls. After a comprehensive interpretation from the multiple algorithms and software, GAPDH paired with RL23 is recommended for the normalization for planktonic larvae and benthic juveniles, but beyond that, TUBB and EF2 are recommended for post-metamorphic stage. Moreover, GAPDH and EF2 were suitable for various pH treatments, and TUBB, RL35 and RL23 could be the alternatives for OA experiments. These results are instrumental for the selection of internal control in Crassostrea hongkongensis during the development, and shed light on other molecular OA experiments in marine invertebrates for reference. Dataset Ocean acidification PANGAEA - Data Publisher for Earth & Environmental Science Pacific ENVELOPE(108.980000,108.980000,21.590000,21.590000) |
institution |
Open Polar |
collection |
PANGAEA - Data Publisher for Earth & Environmental Science |
op_collection_id |
ftpangaea |
language |
English |
topic |
Alkalinity total Animalia Aragonite saturation state Beihai_OA Benthic animals Benthos Bicarbonate ion Calcite saturation state Calculated using seacarb after Nisumaa et al. (2010) Carbon inorganic dissolved Carbonate ion Carbonate system computation flag Carbon dioxide Coast and continental shelf Containers and aquaria (20-1000 L or < 1 m**2) EXP Experiment Fugacity of carbon dioxide (water) at sea surface temperature (wet air) Gene expression (incl. proteomics) Gene name Laboratory experiment Magallana hongkongensis Mollusca North Pacific OA-ICC Ocean Acidification International Coordination Centre Partial pressure of carbon dioxide (water) at sea surface temperature (wet air) pH Salinity Single species Species unique identification unique identification (Semantic URI) unique identification (URI) Stability Temperature water Treatment Tropical Type |
spellingShingle |
Alkalinity total Animalia Aragonite saturation state Beihai_OA Benthic animals Benthos Bicarbonate ion Calcite saturation state Calculated using seacarb after Nisumaa et al. (2010) Carbon inorganic dissolved Carbonate ion Carbonate system computation flag Carbon dioxide Coast and continental shelf Containers and aquaria (20-1000 L or < 1 m**2) EXP Experiment Fugacity of carbon dioxide (water) at sea surface temperature (wet air) Gene expression (incl. proteomics) Gene name Laboratory experiment Magallana hongkongensis Mollusca North Pacific OA-ICC Ocean Acidification International Coordination Centre Partial pressure of carbon dioxide (water) at sea surface temperature (wet air) pH Salinity Single species Species unique identification unique identification (Semantic URI) unique identification (URI) Stability Temperature water Treatment Tropical Type Dang, Xin Noor, Zohaib He, Yuanqiu Lim, Yong-Kian Zhang, Yang Yu, Ziniu Thiyagarajan, Vengatesen Seawater carbonate chemistry and gene expression stability of Hong Kong oyster (Crassostrea hongkongensis) |
topic_facet |
Alkalinity total Animalia Aragonite saturation state Beihai_OA Benthic animals Benthos Bicarbonate ion Calcite saturation state Calculated using seacarb after Nisumaa et al. (2010) Carbon inorganic dissolved Carbonate ion Carbonate system computation flag Carbon dioxide Coast and continental shelf Containers and aquaria (20-1000 L or < 1 m**2) EXP Experiment Fugacity of carbon dioxide (water) at sea surface temperature (wet air) Gene expression (incl. proteomics) Gene name Laboratory experiment Magallana hongkongensis Mollusca North Pacific OA-ICC Ocean Acidification International Coordination Centre Partial pressure of carbon dioxide (water) at sea surface temperature (wet air) pH Salinity Single species Species unique identification unique identification (Semantic URI) unique identification (URI) Stability Temperature water Treatment Tropical Type |
description |
The increase of CO2 by anthropogenic activities leads to a decrease of pH in the ocean surface due to ocean acidification (OA) process. Generally, OA not only reduces the rate of calcification in marine environments but also affects various physiological activities, especially in calcifiers, including edible oysters. Quantitative real-time PCR (qRT-PCR) is often used to detect gene expression in response to OA, which relies on the stability of internal control. However, the appropriate internal controls for OA experiments remain scarce especially in the marine calcifiers. Hence, this study developed internal controls for qRT-PCR assays using the Hong Kong oyster (Crassostrea hongkongensis) as a model to reveal gene expression profile during development under OA. In this study, 17 housekeeping genes were selected as the possible candidate of the internal controls. After a comprehensive interpretation from the multiple algorithms and software, GAPDH paired with RL23 is recommended for the normalization for planktonic larvae and benthic juveniles, but beyond that, TUBB and EF2 are recommended for post-metamorphic stage. Moreover, GAPDH and EF2 were suitable for various pH treatments, and TUBB, RL35 and RL23 could be the alternatives for OA experiments. These results are instrumental for the selection of internal control in Crassostrea hongkongensis during the development, and shed light on other molecular OA experiments in marine invertebrates for reference. |
format |
Dataset |
author |
Dang, Xin Noor, Zohaib He, Yuanqiu Lim, Yong-Kian Zhang, Yang Yu, Ziniu Thiyagarajan, Vengatesen |
author_facet |
Dang, Xin Noor, Zohaib He, Yuanqiu Lim, Yong-Kian Zhang, Yang Yu, Ziniu Thiyagarajan, Vengatesen |
author_sort |
Dang, Xin |
title |
Seawater carbonate chemistry and gene expression stability of Hong Kong oyster (Crassostrea hongkongensis) |
title_short |
Seawater carbonate chemistry and gene expression stability of Hong Kong oyster (Crassostrea hongkongensis) |
title_full |
Seawater carbonate chemistry and gene expression stability of Hong Kong oyster (Crassostrea hongkongensis) |
title_fullStr |
Seawater carbonate chemistry and gene expression stability of Hong Kong oyster (Crassostrea hongkongensis) |
title_full_unstemmed |
Seawater carbonate chemistry and gene expression stability of Hong Kong oyster (Crassostrea hongkongensis) |
title_sort |
seawater carbonate chemistry and gene expression stability of hong kong oyster (crassostrea hongkongensis) |
publisher |
PANGAEA |
publishDate |
2022 |
url |
https://doi.pangaea.de/10.1594/PANGAEA.945551 https://doi.org/10.1594/PANGAEA.945551 |
op_coverage |
LATITUDE: 21.590000 * LONGITUDE: 108.980000 |
long_lat |
ENVELOPE(108.980000,108.980000,21.590000,21.590000) |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
Ocean acidification |
genre_facet |
Ocean acidification |
op_relation |
Dang, Xin; Noor, Zohaib; He, Yuanqiu; Lim, Yong-Kian; Zhang, Yang; Yu, Ziniu; Thiyagarajan, Vengatesen (2022): Internal controls for quantitative RT-PCR analysis of gene expression in response to ocean acidification in edible oysters. Journal of Experimental Marine Biology and Ecology, 548, 151683, https://doi.org/10.1016/j.jembe.2021.151683 Gattuso, Jean-Pierre; Epitalon, Jean-Marie; Lavigne, Héloïse; Orr, James (2021): seacarb: seawater carbonate chemistry with R. R package version 3.2.16. https://cran.r-project.org/web/packages/seacarb/index.html https://doi.pangaea.de/10.1594/PANGAEA.945551 https://doi.org/10.1594/PANGAEA.945551 |
op_rights |
CC-BY-4.0: Creative Commons Attribution 4.0 International Access constraints: unrestricted info:eu-repo/semantics/openAccess |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1594/PANGAEA.945551 https://doi.org/10.1016/j.jembe.2021.151683 |
_version_ |
1766158123090837504 |