CEFAS9ebd811e-d58e-4912-af9c-2c9f225c8999 English dataset Centre for Environment, Fisheries and Aquaculture Science, Lowestoft Laboratory (CEFAS) Cefas Lowestoft Laboratory Pakefield Road Lowestoft Suffolk NR33 0HT UK data.manager@cefas.co.uk pointOfContact 2024-09-24T12:43:19 EPSG Geodetic Parameter Registry 2022-01-07 revision WGS 84 Genetic sequencing data from Scottish environmental samples and reference cultures 2021 2024-09-04 publication 2024-09-24 revision 2024-06-07 creation CEFAS21945 https://data.cefas.co.uk 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. Centre for Environment, Fisheries and Aquaculture Science, Lowestoft Laboratory (CEFAS) Cefas Lowestoft Laboratory Pakefield Road Lowestoft Suffolk NR33 0HT UK data.manager@cefas.co.uk originator Centre for Environment, Fisheries and Aquaculture Science, Lowestoft Laboratory (CEFAS) Cefas Lowestoft Laboratory Pakefield Road Lowestoft Suffolk NR33 0HT UK data.manager@cefas.co.uk custodian Centre for Environment, Fisheries and Aquaculture Science, Lowestoft Laboratory (CEFAS) Cefas Lowestoft Laboratory Pakefield Road Lowestoft Suffolk NR33 0HT UK data.manager@cefas.co.uk distributor Centre for Environment, Fisheries and Aquaculture Science, Lowestoft Laboratory (CEFAS) data.manager@cefas.co.uk owner notPlanned Algal bloom Aquaculture Aquatic environment GEMET, version 1.0 2008-06-01 publication Agricultural and aquaculture facilities Habitats and biotopes GEMET - INSPIRE themes, version 1.0 2008-06-01 publication Unknown SeaVoX Vertical Co-ordinate Coverages 2010-05-18 revision Marine Environmental Data and Information Network MEDIN metadata record availability 2012-01-11 publication data.gov.uk MEDIN metadata record availability 2012-01-11 publication otherRestrictions noLimitations otherRestrictions Public data - no limitations to reuse English environment farming 1.73881 1.74086 52.4581 52.4595 2021-05-24 2021-09-08 Delimited Geographic Information System Unknown https://data.cefas.co.uk/view/21945 Cefas Data Portal download 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. dataset INSPIRE Data Specification on Agricultural and Aquaculture Facilities – Technical Guidelines 2013-12-10 publication false See the referenced specification INSPIRE Data Specification on Habitats and Biotopes – Technical Guidelines 2013-12-10 publication false See the referenced specification Commission Regulation (EU) No 1089/2010 of 23 November 2010 implementing Directive 2007/2/EC of the European Parliament and of the Council as regards interoperability of spatial data sets and services 2010-12-08 publication true See the referenced specification 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 MEDIN 3.1.1