Drosophila C virus genomes, Cambridge (2017)

The resource consists of genome sequence data for the Drosophila C virus that has been serially passaged through different species of Drosophila in the laboratory. The genomes were sequenced and aligned to the reference genome. The frequency of variants at both biallelic and triallelic sites was then calculated. We also generated a phylogeny of the species involved using published data. This data was generated to understand how viruses adapt to new host species by Francis Jiggins and his co workers. The work was carried out between July 2016 and September 2017 and was funded by NERC under award reference NE/L004232/1 Full details about this nonGeographicDataset can be found at https://doi.org/10.5285/4434a27d-5288-4f2e-88ac-4b1372e4d073

Identification info

Metadata Language: English (en)

Character set: utf8

Dataset Reference Date (): 2018-01-24

Identifier: https://catalogue.ceh.ac.uk/id/4434a27d-5288-4f2e-88ac-4b1372e4d073

Identifier: doi: / 10.5285/4434a27d-5288-4f2e-88ac-4b1372e4d073

Other citation details: Jiggins, F.M., Longdon, B. (2018). Drosophila C virus genomes, Cambridge (2017). NERC Environmental Information Data Centre 10.5285/4434a27d-5288-4f2e-88ac-4b1372e4d073

University of Cambridge - Dr Francis Jiggins

University of Cambridge - Jiggins, F.M.

University of Exeter - Longdon, B.

NERC EDS Environmental Information Data Centre

NERC Environmental Information Data Centre

University of Cambridge

Maintenance and update frequency: notPlanned

Keywords

virus
drosophila
DCV
Drosophila C virus
disease emergence
evolution
host shift

Limitations on Public Access: otherRestrictions

Other constraints: no limitations

Use constraints: otherRestrictions

Other constraints: This resource is made available under the terms of the Open Government Licence

Use constraints: otherRestrictions

Other constraints: © Cambridge University

Use constraints: otherRestrictions

Other constraints: If you reuse this data, you should cite: Jiggins, F.M., Longdon, B. (2018). Drosophila C virus genomes, Cambridge (2017). NERC Environmental Information Data Centre https://doi.org/10.5285/4434a27d-5288-4f2e-88ac-4b1372e4d073

Topic category

Health

Begin date: 2016-01-01

End date: 2017-09-01

Distribution Information

Data format

Comma-separated values (CSV) ()
BAM ()
Newick ()

Resource Locator: Supporting information
Supporting information available to assist in re-use of this dataset

Resource Locator: Download the data
Download a copy of this data

Resource Locator: Supporting information
Supporting information available to assist in re-use of this dataset

Resource Locator: Download the data
Download a copy of this data

Quality Scope: nonGeographicDataset

Other: nonGeographicDataset

Report

Dataset Reference Date (): 2010-12-08

Statement: Each species of Drosophila was infected by dipping a needle in virus suspension. After 3 days the fly was then homogenized and the process repeated for 8-10 passages. At the end of this process, Ribonucleic acid (RNA) was extracted, the viral genome amplified by Polymerase chain reaction (PCR) and Nextera libraries constructed. These were sequenced on n Illumina sequencer, the sequences quality trimmed and aligned to the reference genome to generate the BAM file in this dataset. We then called variants to generate the allele frequency CSV files. Full details of these steps are provided in the supporting documentation. NB: these data are not adequately described in that there are no column descriptions for the csv files.

Metadata

File identifier: 4434a27d-5288-4f2e-88ac-4b1372e4d073 XML

Metadata Language: English (en)

Character set: ISO/IEC 8859-1 (also known as Latin 1)

Resource type: nonGeographicDataset

Hierarchy level name: nonGeographicDataset

Metadata Date: 2022-05-20T10:07:22

Metadata standard name: UK GEMINI

Metadata standard version: 2.3

Environmental Information Data Centre

Lancaster Environment Centre, Library Avenue, Bailrigg , Lancaster , LA1 4AP , UK

Overviews

Publishing Body

Access the portal

Full access to the portal and metadata.

Associated resources (if any)

Not available

Default