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  "author": "de Wit, Pierre",
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  "author": "de Wit, Pierre",
            
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  "author_email": "",
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  "author_email": "",
            
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  "citation": [],
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  "citation": [],
            
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  "creator_user_id": "17755db4-395a-4b3b-ac09-e8e3484ca700",
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  "creator_user_id": "17755db4-395a-4b3b-ac09-e8e3484ca700",
            
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  "doi": "10.1594/PANGAEA.893428",
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  "doi": "10.1594/PANGAEA.893428",
            
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  "doi_date_published": "2018",
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  "doi_date_published": "2018",
            
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  "doi_publisher": "",
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  "doi_publisher": "",
            
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  "doi_status": "True",
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  "doi_status": "True",
            
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  "extra_authors": [
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  "extra_authors": [
            
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    {
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    {
            
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      "extra_author": "Durland, Evan",
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      "extra_author": "Durland, Evan",
            
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      "familyName": "Durland",
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      "familyName": "Durland",
            
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      "givenName": "Evan",
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      "givenName": "Evan",
            
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      "orcid": ""
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      "orcid": ""
            
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    },
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    },
            
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    {
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    {
            
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      "extra_author": "Ventura, Alexander",
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      "extra_author": "Ventura, Alexander",
            
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      "familyName": "Ventura",
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      "familyName": "Ventura",
            
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      "givenName": "Alexander",
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      "givenName": "Alexander",
            
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      "orcid": ""
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      "orcid": ""
            
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    },
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    },
            
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    {
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    {
            
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      "extra_author": "Langdon, Chris",
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      "extra_author": "Langdon, Chris",
            
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      "familyName": "Langdon",
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      "familyName": "Langdon",
            
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      "givenName": "Chris",
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      "givenName": "Chris",
            
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      "orcid": "0000-0002-3043-3806"
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      "orcid": "0000-0002-3043-3806"
            
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    }
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    }
            
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  ],
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  ],
            
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  "familyName": "de Wit",
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  "familyName": "de Wit",
            
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  "givenName": "Pierre",
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  "givenName": "Pierre",
            
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  "license_id": "CC-BY-3.0",
            
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  "license_title": "CC-BY-3.0",
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  "license_title": "CC-BY-3.0",
            
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  "metadata_created": "2024-11-29T11:46:08.224355",
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  "metadata_modified": "2024-11-29T11:46:08.224361",
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  "metadata_modified": "2024-11-30T10:44:14.862040",
            
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  "name": "png-doi-10-1594-pangaea-893428",
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  "name": "png-doi-10-1594-pangaea-893428",
            
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  "notes": "Background: Despite recent work to characterize gene 
40
  "notes": "Background: Despite recent work to characterize gene 
            
41
expression changes associated with larval development in oysters, the 
41
expression changes associated with larval development in oysters, the 
            
42
mechanism by which the larval shell is first formed is still largely 
42
mechanism by which the larval shell is first formed is still largely 
            
43
unknown. In Crassostrea gigas, this shell forms within the first 24 h 
43
unknown. In Crassostrea gigas, this shell forms within the first 24 h 
            
44
post fertilization, and it has been demonstrated that changes in water 
44
post fertilization, and it has been demonstrated that changes in water 
            
45
chemistry can cause delays in shell formation, shell deformations and 
45
chemistry can cause delays in shell formation, shell deformations and 
            
46
higher mortality rates. In this study, we use the delay in shell 
46
higher mortality rates. In this study, we use the delay in shell 
            
47
formation associated with exposure to CO2-acidified seawater to 
47
formation associated with exposure to CO2-acidified seawater to 
            
48
identify genes correlated with initial shell deposition.\nResults: By 
48
identify genes correlated with initial shell deposition.\nResults: By 
            
49
fitting linear models to gene expression data in ambient and low 
49
fitting linear models to gene expression data in ambient and low 
            
50
aragonite saturation treatments, we are able to isolate 37 annotated 
50
aragonite saturation treatments, we are able to isolate 37 annotated 
            
51
genes correlated with initial larval shell formation, which can be 
51
genes correlated with initial larval shell formation, which can be 
            
52
categorized into 1) ion transporters, 2) shell matrix proteins and 3) 
52
categorized into 1) ion transporters, 2) shell matrix proteins and 3) 
            
53
protease inhibitors. Clustering of the gene expression data into 
53
protease inhibitors. Clustering of the gene expression data into 
            
54
co-expression networks further supports the result of the linear 
54
co-expression networks further supports the result of the linear 
            
55
models, and also implies an important role of dynein motor proteins as 
55
models, and also implies an important role of dynein motor proteins as 
            
56
transporters of cellular components during the initial shell formation 
56
transporters of cellular components during the initial shell formation 
            
57
process.\nConclusions: Using an RNA-Seq approach with high temporal 
57
process.\nConclusions: Using an RNA-Seq approach with high temporal 
            
58
resolution allows us to identify a conceptual model for how oyster 
58
resolution allows us to identify a conceptual model for how oyster 
            
59
larval calcification is initiated. This work provides a foundation for 
59
larval calcification is initiated. This work provides a foundation for 
            
60
further studies on how genetic variation in these identified genes 
60
further studies on how genetic variation in these identified genes 
            
61
could affect fitness of oyster populations subjected to future 
61
could affect fitness of oyster populations subjected to future 
            
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environmental changes, such as ocean acidification.",
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environmental changes, such as ocean acidification.",
            
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data from earth system research. PANGAEA guarantees long-term 
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data and metadata, a high degree of structural and semantic 
            
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hosting institutions ensures FAIRness of archived data.",
            
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  "publication_year": "2018",
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    {
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      "authors": "de Wit Pierre,Durland Evan,Ventura Alexander,Langdon 
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      "authors": "de Wit Pierre,Durland Evan,Ventura Alexander,Langdon 
            
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Chris",
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Chris",
            
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      "email_authors": 
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      "email_authors": 
            
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t@marine.gu.se,durlandevan@gmail.com,alexander.ventura@bioenv.gu.se,",
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t@marine.gu.se,durlandevan@gmail.com,alexander.ventura@bioenv.gu.se,",
            
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      "identifier": "https://doi.org/10.1186/s12864-018-4519-y",
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      "identifier": "https://doi.org/10.1186/s12864-018-4519-y",
            
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      "identifier_type": "DOI",
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      "identifier_type": "DOI",
            
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      "orcid_authors": "0000-0003-4709-3438,,,0000-0002-3043-3806",
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      "source": "BMC Genomics",
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      "source": "BMC Genomics",
            
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      "title": "Gene expression correlated with delay in shell 
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      "title": "Gene expression correlated with delay in shell 
            
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formation in larval Pacific oysters (Crassostrea gigas) exposed to 
104
formation in larval Pacific oysters (Crassostrea gigas) exposed to 
            
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experimental ocean acidification provides insights into shell 
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experimental ocean acidification provides insights into shell 
            
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formation mechanisms",
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formation mechanisms",
            
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      "year": "2018"
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      "year": "2018"
            
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      "authors": "Gattuso Jean-Pierre,Epitalon Jean-Marie,Lavigne 
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H\u00e9lo\u00efse,Orr James C,Gentili Bernard,Proye 
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H\u00e9lo\u00efse,Orr James C,Gentili Bernard,Proye 
            
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Aur\u00e9lien,Soetaert Karline,Rae James",
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Aur\u00e9lien,Soetaert Karline,Rae James",
            
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      "email_authors": 
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      "title": "Data of figure 3: weighted gene correlation network 
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      "title": "Data of figure 3: weighted gene correlation network 
            
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modules and normalized expression levels",
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modules and normalized expression levels",
            
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      "authors": "Gattuso Jean-Pierre,Epitalon Jean-Marie,Lavigne 
            
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H\u00e9lo\u00efse,Orr James C,Gentili Bernard,Proye 
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H\u00e9lo\u00efse,Orr James C,Gentili Bernard,Proye 
            
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Aur\u00e9lien,Soetaert Karline,Rae James",
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      "source": "",
            
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      "title": "seacarb: seawater carbonate chemistry with R. R 
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      "display_name": "Calcification-Dissolution",
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194
      "display_name": "Calcification",
            
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      "id": "90f00008-2fad-42d6-b697-f331b63dca60",
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      "id": "7e8ea514-3848-498c-b07f-22d71e1b83e3",
            
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      "name": "Calcification-Dissolution",
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      "name": "Calcification",
            
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      "state": "active",
197
      "state": "active",
            
191
      "vocabulary_id": null
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      "vocabulary_id": null
            
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    },
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    },
            
193
    {
200
    {
            
194
      "display_name": "Coast and continental shelf",
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      "display_name": "Coast and continental shelf",
            
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      "id": "58eb1929-34b5-4fd9-ac44-824f0e51de40",
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      "id": "58eb1929-34b5-4fd9-ac44-824f0e51de40",
            
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      "name": "Coast and continental shelf",
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      "name": "Coast and continental shelf",
            
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      "state": "active",
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      "state": "active",
            
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      "vocabulary_id": null
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      "vocabulary_id": null
            
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    },
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    },
            
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    {
207
    {
            
201
      "display_name": "Crassostrea gigas",
208
      "display_name": "Crassostrea gigas",
            
202
      "id": "44a90705-8dc8-41ad-a3c4-d60cdbce94bf",
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      "id": "44a90705-8dc8-41ad-a3c4-d60cdbce94bf",
            
203
      "name": "Crassostrea gigas",
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      "name": "Crassostrea gigas",
            
t
t
211
      "state": "active",
            
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      "vocabulary_id": null
            
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    },
            
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    {
            
215
      "display_name": "Dissolution",
            
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      "id": "ccf682ce-0609-42e9-87cd-0873f6fce3f5",
            
217
      "name": "Dissolution",
            
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      "state": "active",
218
      "state": "active",
            
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      "vocabulary_id": null
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      "vocabulary_id": null
            
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    },
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    },
            
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    {
221
    {
            
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      "display_name": "Gene expression incl. proteomics",
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      "display_name": "Gene expression incl. proteomics",
            
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      "id": "a266e76f-1f2a-427a-97e6-8e248d591f17",
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      "id": "a266e76f-1f2a-427a-97e6-8e248d591f17",
            
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      "name": "Gene expression incl. proteomics",
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      "name": "Gene expression incl. proteomics",
            
211
      "state": "active",
225
      "state": "active",
            
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      "vocabulary_id": null
226
      "vocabulary_id": null
            
213
    },
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    },
            
214
    {
228
    {
            
215
      "display_name": "Laboratory experiment",
229
      "display_name": "Laboratory experiment",
            
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      "id": "c6c00754-c769-4932-a517-bff2c9512884",
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      "id": "c6c00754-c769-4932-a517-bff2c9512884",
            
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      "name": "Laboratory experiment",
231
      "name": "Laboratory experiment",
            
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      "state": "active",
232
      "state": "active",
            
219
      "vocabulary_id": null
233
      "vocabulary_id": null
            
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    },
234
    },
            
221
    {
235
    {
            
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      "display_name": "Mollusca",
236
      "display_name": "Mollusca",
            
223
      "id": "006d5f6d-11b3-4c34-a35a-879d7cd074c8",
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      "id": "006d5f6d-11b3-4c34-a35a-879d7cd074c8",
            
224
      "name": "Mollusca",
238
      "name": "Mollusca",
            
225
      "state": "active",
239
      "state": "active",
            
226
      "vocabulary_id": null
240
      "vocabulary_id": null
            
227
    },
241
    },
            
228
    {
242
    {
            
229
      "display_name": "North Pacific",
243
      "display_name": "North Pacific",
            
230
      "id": "efbdbaff-aa72-4a57-8e03-e9f84253d644",
244
      "id": "efbdbaff-aa72-4a57-8e03-e9f84253d644",
            
231
      "name": "North Pacific",
245
      "name": "North Pacific",
            
232
      "state": "active",
246
      "state": "active",
            
233
      "vocabulary_id": null
247
      "vocabulary_id": null
            
234
    },
248
    },
            
235
    {
249
    {
            
236
      "display_name": "Pelagos",
250
      "display_name": "Pelagos",
            
237
      "id": "012f5b69-4e75-4f54-8ac4-8bf192cafaa2",
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      "id": "012f5b69-4e75-4f54-8ac4-8bf192cafaa2",
            
238
      "name": "Pelagos",
252
      "name": "Pelagos",
            
239
      "state": "active",
253
      "state": "active",
            
240
      "vocabulary_id": null
254
      "vocabulary_id": null
            
241
    },
255
    },
            
242
    {
256
    {
            
243
      "display_name": "Single species",
257
      "display_name": "Single species",
            
244
      "id": "88de69be-3bdd-4cf8-b6a1-386d72c5888d",
258
      "id": "88de69be-3bdd-4cf8-b6a1-386d72c5888d",
            
245
      "name": "Single species",
259
      "name": "Single species",
            
246
      "state": "active",
260
      "state": "active",
            
247
      "vocabulary_id": null
261
      "vocabulary_id": null
            
248
    },
262
    },
            
249
    {
263
    {
            
250
      "display_name": "Temperate",
264
      "display_name": "Temperate",
            
251
      "id": "31aaeb0c-a4a5-4a8e-9c90-be1eff0cac91",
265
      "id": "31aaeb0c-a4a5-4a8e-9c90-be1eff0cac91",
            
252
      "name": "Temperate",
266
      "name": "Temperate",
            
253
      "state": "active",
267
      "state": "active",
            
254
      "vocabulary_id": null
268
      "vocabulary_id": null
            
255
    },
269
    },
            
256
    {
270
    {
            
257
      "display_name": "Zooplankton",
271
      "display_name": "Zooplankton",
            
258
      "id": "9a829b96-807f-48c1-84c6-8fa50a64f5a5",
272
      "id": "9a829b96-807f-48c1-84c6-8fa50a64f5a5",
            
259
      "name": "Zooplankton",
273
      "name": "Zooplankton",
            
260
      "state": "active",
274
      "state": "active",
            
261
      "vocabulary_id": null
275
      "vocabulary_id": null
            
262
    }
276
    }
            
263
  ],
277
  ],
            
264
  "title": "Seawater carbonate chemistry and gene expression, shell 
278
  "title": "Seawater carbonate chemistry and gene expression, shell 
            
265
formation in larval Pacific oysters (Crassostrea gigas)",
279
formation in larval Pacific oysters (Crassostrea gigas)",
            
266
  "type": "vdataset",
280
  "type": "vdataset",
            
267
  "url": "https://doi.org/10.1594/PANGAEA.893428"
281
  "url": "https://doi.org/10.1594/PANGAEA.893428"
            
268
}
282
}