TemperateReefBase Geonetwork Catalogue
Population genetics dataset for Antarctic krill (Euphausia superba): Restriction site-associated DNA sequencing (RAD-seq) and mtDNA sequencing
This restriction site associated DNA sequencing (RAD-seq) dataset for Antarctic krill (Euphausia superba) includes raw sequence data and summaries for 148 krill from 5 Southern Ocean sites. A detailed README.pdf file is provided to describe components of the dataset. DNA library preparation was carried out in two separate batches by Floragenex (Eugene, Oregon, USA). RAD fragment libraries (SbfI) were sequenced on an Illumina HiSeq 2000 using single-end 100 bp chemistry. As there is no reference genome for Antarctic krill, a set of unique 90 bp sequences (RAD tags) was assembled from 17.3 million single-end reads from an individual krill. We obtained over a billion raw reads from the 148 krill in our study (a mean of 6.8 million reads per sample). The reference assembly contained 239,441 distinct RAD tags. The core genotype dataset exported for downstream data filtering included just those SNPs with genotype calls in at least 80% of the krill samples and contained 12,114 SNPs on 816 RAD tags.
Sample collection table (comma separated):
Southern Ocean Location, Sample Size, Austral Summer, Latitude, Longitude, ID
East Antarctica (Casey), 21, 2010/2011, 64S, 100E, Cas
East Antarctica (Mawson), 22, 2011/2012. 66S, 70E, Maw
Lazarev Sea, 38, 2004/2005 and 2007/2008, 66S, 0E, Laz
Western Antarctic Peninsula, 16, 2010/2011, 69S, 76W, WAP
Ross Sea, 23, 2012/2013, 68S, 178E, Ross
Simple
Identification info
- Alternate title
- Population genetics dataset for Antarctic krill (Euphausia superba): Restriction site-associated DNA sequencing (RAD-seq) and mtDNA sequencing
- Date (Publication)
- 2015-09-09
- Edition
- 1
- Citation identifier
-
Dataset DOI
- Title
- Information and documentation - Digital object identifier system
- Date (Publication)
- 2012-04-23
- Citation identifier
- ISO 26324:2012
- Citation identifier
- doi:10.4225/15/556FAB354BE19
Originator
Publisher
Principal investigator
Collaborator
- Name
- CAASM Metadata
- Status
- Completed
Custodian
- Topic category
-
- Biota
- Oceans
Extent
))
Extent
- Description
- Temporal Coverage
Temporal extent
- TimePeriod
- 2012-01-01 2013-12-31
- NASA/GCMD Earth Science Keywords
-
- EARTH SCIENCE > BIOLOGICAL CLASSIFICATION > ANIMALS/INVERTEBRATES > ARTHROPODS > CRUSTACEANS > EUPHAUSIIDS (KRILL)
- Keywords
-
- Genome
- DNA
- NASA/GCMD Earth Science Keywords
-
- ADS > Automated DNA Sequencer
- NASA/GCMD Earth Science Keywords
-
- LABORATORY
- SHIPS
- NASA/GCMD Earth Science Keywords
-
- AMD
- AMD/AU
- CEOS
- NASA/GCMD Earth Science Keywords
-
- CONTINENT > ANTARCTICA
- OCEAN > SOUTHERN OCEAN
- GEOGRAPHIC REGION > POLAR
Resource constraints
- Use limitation
- This metadata record is publicly available.
Resource constraints
- Access constraints
- licence
- Other constraints
- These data are publicly available, but due to their size are stored offline, and are available on request to the Australian Antarctic Data Centre.
Resource constraints
- File type
- Portable Network Graphic
- Title
- Attribution 4.0 International (CC BY 4.0)
- Website
-
https://creativecommons.org/licenses/by/4.0/legalcode
Legal code for Creative Commons by Attribution 4.0 International license
- Use constraints
- licence
- Other constraints
- This data set conforms to the CCBY Attribution License (http://creativecommons.org/licenses/by/4.0/). Please follow instructions listed in the citation reference provided at http://data.aad.gov.au/aadc/metadata/citation.cfm?entry_id=AAS_4015_Population_Genetics when using these data.
- Language
- English
- Character encoding
- UTF8
Distribution Information
Distributor
Distributor
Distributor
- Fees
- Free
- Planned available datetime
- 2015-09-09T00:00:00
- Units of distribution
- GB
- Transfer size
- 220
- Distribution format
-
- Text, csv, PDF
- OnLine resource
-
GET DATA
Request point for the data
- OnLine resource
-
PROJECT HOME PAGE
Public information for AAS project 4015
- OnLine resource
-
VIEW RELATED INFORMATION
Citation reference for this metadata record and dataset
Resource lineage
- Statement
- DNA sequencing done by: Floragenex, Inc. 4725 Village Plaza Loop, Suite 200 Eugene, OR 97401 USA Most of the SNP markers were from multi-copy genomic regions.
- Hierarchy level
- Dataset
- Maintenance and update frequency
- As needed
- Maintenance note
- 2015-06-04 - record created by Dave Connell from a template completed by Bruce Deagle. 2015-09-09 - record updated by Dave Connell to publicly release the data.
Metadata
- Metadata identifier
- string/AAS_4015_Population_Genetics
- Language
- English
- Character encoding
- UTF8
Author
Sponsor
Owner
Type of resource
- Resource scope
- Dataset
Alternative metadata reference
- Title
- gov.nasa.gsfc.gcmd
- Citation identifier
- fab59858-0d32-4709-ab33-fa9f776ce3b7
Alternative metadata reference
- Title
- gov.nasa.gsfc.gcmd
- Date (Last Revision)
- 2015-11-30T03:59:16
Identifier
- Description
- metadata.extraction_date
Alternative metadata reference
- Title
- gov.nasa.gsfc.gcmd
- Citation identifier
- 8.6
- Metadata linkage
-
http://data.aad.gov.au/metadata/records/AAS_4015_Population_Genetics
Point of truth for the metadata record
- Date info (Creation)
- 2015-06-03T00:00:00
- Date info (Last Update)
- 2017-04-26
Metadata standard
- Title
- ISO 19115-3
- Edition
- 2014
- Other citation details
- Version 1
- Title
- DIF to ISO 19115-1 Profile
Overviews
Spatial extent
Provided by
