Identification

Title

Genetic sequencing data from Scottish environmental samples and reference cultures 2021

Abstract

Sequencing data from environmental samples and reference cultures, including paralytic shellfish toxin data and environmental cell counts, published by the Food Standards Scotland as part of the routine monitoring programme.

Resource type

dataset

Resource locator

https://data.cefas.co.uk/view/21945

name: Cefas Data Portal

description: The Cefas Data Portal contains metadata records and data sets available to download and connect to in support of our commitment to open science. Data is available in the following formats: CSV, ESRI Shapefile. The data can also be accessed via the WFS and WMS protocols.

function: download

Unique resource identifier

code

CEFAS21945

codeSpace

https://data.cefas.co.uk

Dataset language

eng

Spatial reference system

code identifying the spatial reference system

Classification of spatial data and services

Topic category

environment

farming

Keywords

Keyword set

keyword value

originating controlled vocabulary

title

reference date

date type

publication

effective date

2008-06-01

Keyword set

keyword value

originating controlled vocabulary

title

reference date

date type

publication

effective date

2008-06-01

Keyword set

keyword value

originating controlled vocabulary

title

reference date

date type

revision

effective date

2010-05-18

Keyword set

keyword value

originating controlled vocabulary

title

reference date

date type

publication

effective date

2012-01-11

Keyword set

keyword value

originating controlled vocabulary

title

reference date

date type

publication

effective date

2012-01-11

Geographic location

West bounding longitude

1.73881

East bounding longitude

1.74086

North bounding latitude

52.4595

South bounding latitude

52.4581

Temporal reference

Temporal extent

Begin position

2021-05-24

End position

2021-09-08

Dataset reference date

date type

publication

effective date

2024-09-04

date type

revision

effective date

2024-09-24

date type

creation

effective date

2024-06-07

Frequency of update

notPlanned

Quality and validity

Lineage

The samples were collected as part of the routine monitoring programme on behalf of Food Standards Scotland and were done so in accordance with European Union regulations: Regulation (EU) 2019/627 of 15 March 2019 laying down uniform practical arrangements for the performance of official controls on products of animal origin intended for human consumption in accordance with Regulation (EU) 2017/625 of the European Parliament and of the Council and amending Commission Regulation (EC) No 2074/2005 as regards official controls. Analysis of shellfish flesh for paralytic shellfish toxins was performed using pre-column oxidation with fluorescence detection, cell counts were performed on Lugol's fixed water samples in a Sedgwick Rafter settlement chamber. All routine analysis was performed under in accordance with UKAS accreditation. Sequencing was performed on the same Lugol's fixed samples as used for the cell counts and was done using Nanopore sequencing technologies MinION MK 1B and a custom computing device out lined in the link above. In brief, the assay used isothermal amplification to target Alexandrium DNA for sequencing, once generated, the sequencing data were compared to a reference, list providing real time identification of species likely to be present and also the ability to confirm this data using further bio-informatic tools. The data generated for this study and that taken from the routine monitoring programme were anonymised to ensure there is no negative impact harvesters from study areas. The locations are available in the internal data and as such should not be shared externally without removal of site names. The manuscript identifies the sampling sites as follows "The environmental study made use of legacy material collected in 2021 as part of the routine monitoring program by Scottish Association of Marine Science, Oban, Scotland on behalf of Food Standards Scotland". The manuscript is published in MDPI-Toxins: `Toxins | Free Full-Text | Combining Nanopore Sequencing with Recombinase Polymerase Amplification Enables Identification of Dinoflagellates from the Alexandrium Genus, Providing a Rapid, Field Deployable Tool (mdpi.com)`_. Sequencing data generated from the study was compared to the existing (and published) routine monitoring data to see how the assay used could add value to routine monitoring processes. The assay used isothermal amplification to target Alexandrium DNA for sequencing, once data was generated, the resulting sequences were compared to a reference list providing real time identification of species likely to be present and also the ability to confirm this data using further bio-informatic tools. This allowed the rapid low cost an .. _`toxins | free full-text | combining nanopore sequencing with recombinase polymerase amplification enables identification of dinoflagellates from the alexandrium genus, providing a rapid, field deployable tool (mdpi.com)`: https://www.mdpi.com/2072-6651/15/6/372

Conformity

Conformity report

specification

title

reference date

date type

publication

effective date

2013-12-10

degree

false

explanation

See the referenced specification

Conformity report

specification

title

reference date

date type

publication

effective date

2013-12-10

degree

false

explanation

See the referenced specification

Conformity report

specification

title

reference date

date type

publication

effective date

2010-12-08

degree

true

explanation

See the referenced specification

Data format

name of format

Unknown

version of format

Constraints related to access and use

Constraint set

Limitations on public access

Constraint set

Limitations on public access

Responsible organisations

Responsible party

organisation name

Centre for Environment, Fisheries and Aquaculture Science, Lowestoft Laboratory (CEFAS)

full postal address

Cefas Lowestoft Laboratory

Pakefield Road

Lowestoft

NR33 0HT

UK

email address

data.manager@cefas.co.uk

responsible party role

originator

Responsible party

organisation name

Centre for Environment, Fisheries and Aquaculture Science, Lowestoft Laboratory (CEFAS)

full postal address

Cefas Lowestoft Laboratory

Pakefield Road

Lowestoft

NR33 0HT

UK

email address

data.manager@cefas.co.uk

responsible party role

custodian

Responsible party

organisation name

Centre for Environment, Fisheries and Aquaculture Science, Lowestoft Laboratory (CEFAS)

full postal address

Cefas Lowestoft Laboratory

Pakefield Road

Lowestoft

NR33 0HT

UK

email address

data.manager@cefas.co.uk

responsible party role

distributor

Responsible party

organisation name

Centre for Environment, Fisheries and Aquaculture Science, Lowestoft Laboratory (CEFAS)

email address

data.manager@cefas.co.uk

responsible party role

owner

Metadata on metadata

Metadata point of contact

organisation name

Centre for Environment, Fisheries and Aquaculture Science, Lowestoft Laboratory (CEFAS)

full postal address

Cefas Lowestoft Laboratory

Pakefield Road

Lowestoft

NR33 0HT

UK

email address

data.manager@cefas.co.uk

responsible party role

pointOfContact

Metadata date

2024-09-24T12:43:19

Metadata language