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Metadata: 2020, Glen Wheeler, The Marine Biological Association of the UK (MBA) Coccolithus braarudii life cycle protein mass spectrometry
Abstract:
Coccolithophores are crucial for marine biogeochemical cycling. However, much of their physiology remains poorly understood, particularly their elusive haplo-diplontic life cycle. We aimed to characterise differences between HET and HOL Coccolithus braarudii by carrying out protein mass spectrometry of both life phases. We found that the proteome was substantially different and characterized novel physiological mechanisms.
Data holder:
Data Archive for Seabed Species and Habitats (DASSH)
Use constraints:
open access
| Other details | ||
| Internal code | Internally assigned metadata identifier | 1906 |
| Title | The title is used to provide a brief and precise description of the dataset such as 'Date', 'Originating organisation/programme', 'Location' and 'Type of survey'. All acronyms and abbreviations should be reproduced in full. | 2020, Glen Wheeler, The Marine Biological Association of the UK (MBA) Coccolithus braarudii life cycle protein mass spectrometry |
| File Identifier | The File Identifier is a code, preferably a GUID, that is globally unique and remains with the same metadata record even if the record is edited or transferred between portals or tools. | 831fa9bbcd9d6bb3c6d8fca5400a10a1 |
| Resource Identifier | This is the code assigned by the data owner. | DASSHDT00000529 |
| Resource type | The resource type will likely be a dataset but could also be a series (collection of datasets with a common specification) or a service. | dataset |
| Start date | This describes the date the resource starts. This may only be the year if month and day are not known | 2020-07-01 |
| End date | This describes the date the resource ends. This may only be the year if month and day are not known | 2021-04-01 |
| Spatial resolution | This describes the spatial resolution of the dataset or the spatial limitations of the service. | inapplicable |
| Frequency of updates | This describes the frequency with which the resource is modified or updated i.e. a monitoring programme that samples once per year has a frequency that is described as 'annually'. | notPlanned |
| Abstract | The abstract provides a clear and brief statement of the content of the resource. | Coccolithophores are crucial for marine biogeochemical cycling. However, much of their physiology remains poorly understood, particularly their elusive haplo-diplontic life cycle. We aimed to characterise differences between HET and HOL Coccolithus braarudii by carrying out protein mass spectrometry of both life phases. We found that the proteome was substantially different and characterized novel physiological mechanisms. |
| Lineage | Lineage includes the background information, history of the sources of data, data quality statements and methods. | Coccolithophore culturing, harvesting, and protein extraction - Haploid and diploid cultures of C. braarudii were cultured at 15 degrees celsius and harvested during mid-exponential growth. Proteins were extracted using RIPA buffer and liquid nitrogen grinding. Coccolithophore protein mass spectrometry (MS) - TMT labelling, Liquid Chromatography Mass Spectrometry and subsequent raw data analysis were carried out by the Proteomics Facility of Bristol University, UK. The raw data files were processed and quantified using Proteome Discoverer software v2.1 (Thermo Scientific) and searched against the latest release version 2021_2 of the C. braarudii predicted protein database (25204 proteins) from Uniprot (www.uniprot.org), and a common contaminates database using the SEQUEST HT algorithm. The reverse database search option was enabled, and all data was filtered to satisfy false discovery rate (FDR) of 5 percent, which is classed as FDR confidence = Medium. Data were normalized to the total peptide amount in each sample by Proteome Discoverer to equalize peptide abundances across all TMT channels and correcting for differences in sample loading. Normalized proteins were subsequently quality controlled. Differential abundance between life phases was assessed using LIMMA (Ritchie et al., 2015), with a significance level of less than 0.05. Notes on the data spreadsheet - Accession: Uniprot Accession Number for Coccolithus braarudii logFC, AveExpr, t, P.Value, adj.P.Val, B - For information on analysing RNAseq or protein MS data, see package LIMMA: https://kasperdanielhansen.github.io/genbioconductor/html/limma.html Unique Peptides - Number of unique peptide for each protein Protein FDR Confidence: False discovery rate (FDR), 5 percent = Medium, 1 percent = High Blast2GO - Protein annotation Description - Protein description from Uniprot Best BLAST hit and e value: NCBI Blast hit with highest e-value |
| Related keywords | ||
| Keyword | General subject area(s) associated with the resource, uses multiple controlled vocabularies | Marine Environmental Data and Information Network |
| General subject area(s) associated with the resource, uses multiple controlled vocabularies | NDGO0005 | |
| Keyword title | data.gov.uk | |
| Keyword | General subject area(s) associated with the resource, uses multiple controlled vocabularies | Species distribution |
| General subject area(s) associated with the resource, uses multiple controlled vocabularies | Biodiversity | |
| General subject area(s) associated with the resource, uses multiple controlled vocabularies | Phytoplankton generic abundance in water bodies | |
| Geographical coverage | ||
| North | The northern-most limit of the data resource in decimal degrees | 50.3647 |
| East | The eastern-most limit of the data resource in decimal degrees | -4.1382 |
| South | The southern-most limit of the data resource in decimal degrees | 50.3638 |
| West | The western-most limit of the data resource in decimal degrees | -4.1398 |
| Responsible organisations | ||
| Role | The point of contact is person or organisation with responsibility for the creation and maintenance of the metadata for the resource. | pointOfContact |
| Organisation name | Data Archive for Seabed Species and Habitats (DASSH) | |
| Position name | Data Manager | |
| Phone | 01752 633102 | |
| Fax | 01752 633291 | |
| Delivery point | Marine Biological Association of the UK, The Laboratory, Citadel Hill | |
| Postal code | PL1 2PB | |
| City | Plymouth | |
| dassh.enquiries@mba.ac.uk | ||
| Role | The distributor is the person or organisation that distributes the resource. | distributor |
| Organisation name | Data Archive for Seabed Species and Habitats (DASSH) | |
| Position name | Data Manager | |
| Phone | 01752 633102 | |
| Fax | 01752 633291 | |
| Delivery point | Marine Biological Association of the UK, The Laboratory, Citadel Hill | |
| Postal code | PL1 2PB | |
| City | Plymouth | |
| dassh.enquiries@mba.ac.uk | ||
| Role | The originator is the person or organisation who created, collected or produced the resource. | originator |
| Organisation name | Marine Biological Association of the United Kingdom | |
| Individual name | Daniela Sturm | |
| danstu@mba.ac.uk | ||
| Role | The custodian is the person or organisation that accepts responsibility for the resource and ensures appropriate care and maintenance. If a dataset has been lodged with a Data Archive Centre for maintenance then this organisation is be entered here. | custodian |
| Organisation name | Data Archive for Seabed Species and Habitats (DASSH) | |
| Position name | Data Manager | |
| Phone | 01752 633102 | |
| Fax | 01752 633291 | |
| Delivery point | Marine Biological Association of the UK, The Laboratory, Citadel Hill | |
| Postal code | PL1 2PB | |
| City | Plymouth | |
| dassh.enquiries@mba.ac.uk | ||
| Resource locators | ||
| Locator URL | Web address (URL) that links to the resource | http://doi.org/10.17031/65afd01b4e0e2.1 |
| Locator name | Name of the web resource | DOI link |
| Locator URL | Web address (URL) that links to the resource | http://www.dassh.ac.uk |
| Locator name | Name of the web resource | DASSH Website |
| Dataset constraints | ||
| 20 Limitations on Public Access - Access constraints | otherRestrictions | |
| 20 Limitations on Public Access - Other constraints | This states any limitations on access to the data and uses free text. | open access |
| 21 Conditions for Access and Use - Use limitation | This states any constraints on use of the data. Multiple conditions can be recorded for different parts of the data resource. If no conditions apply, then `No condtions apply` is recorded. This uses free text. | CC BY |
| Version info | ||
| Date of publication | The publication date of the resource or if previously unpublished the date that the resource was made publicly available via the MEDIN network. | 2024-02-01 |
| Date of last revision | The most recent date that the resource was revised. | 2021-04-01 |
| Date of creation | The date that the resource was created. | 2021-04-01 |
| Harvest date | The date which this record has been (re)harvested from the provider. | 2026-04-12 |
| Metadata date | The date when the content of this metadata record was last updated. | 2024-05-21 |
| Metadata standard name | The name of the metadata standard used to create this metadata | MEDIN Discovery metadata standard |
| Metadata standard version | The version of the MEDIN Discovery Metadata Standard used to create the metadata record | 2.3.8 |