Data · collection · 2015
Population genetics dataset for Antarctic krill (Euphausia superba): Restriction site-associated DNA sequencing (RAD-seq) and mtDNA sequencing
Listed in NASA Earthdata CMR
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.
Description
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).
Read the rest (1 more)
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
Links
Get the data
- Request point for the data data.aad.gov.au/aadc/portal/download_file.cfm?file_id=4463 ↗
download · from NASA CMR
Where it is published
- DOI doi.org/10.4225/15/556fab354be19 ↗
DOI / persistent id · from NASA CMR
Documentation and papers
- data.aad.gov.au /aadc/metadata/citation.cfm?entry_id=AAS_4015_Population_Geneti… ↗
Citation reference for this metadata record and dataset
documentation · from NASA CMR
- Public information for AAS project 4015 secure3.aad.gov.au/proms/public/projects/report_project_public.cfm?project_no=4015 ↗
project · from NASA CMR
Catalogue records · 2
- CMR UMM-JSON cmr.earthdata.nasa.gov/search/concepts/C1214311662-AU_AADC.umm_json ↗
metadata API · from NASA CMR
- CMR record cmr.earthdata.nasa.gov/search/concepts/C1214311662-AU_AADC.html ↗
catalogue entry · from NASA CMR
Topics
- Stated by source
- Automated DNA Sequencer · Euphausiids Krill · LABORATORY · Not provided · SHIPS
- Inferred from text
- Sequencing 75% · Tabular 65%
Provenance · 1 source records, 15 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| NASA Earthdata CMR | C1214311662-AU_AADC | 15 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · NASA CMR | connector:nasa_cmr@1.0.0 | |
| concepts[instrument].gcmd_instrument:ads | source · NASA CMR | connector:nasa_cmr@1.0.0 | |
| concepts[measured_variable].gcmd:earth-science/biological-classification/animals-invertebrates/arthropods/crustaceans/euphausiids-krill | source · NASA CMR | connector:nasa_cmr@1.0.0 | |
| concepts[modality].local:modality:sequencing | enrichment · NASA CMR | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[modality].local:modality:tabular | enrichment · NASA CMR | keyword-concept-rules@1.0.0 | title+description (65%) |
| concepts[platform].gcmd_platform:laboratory | source · NASA CMR | connector:nasa_cmr@1.0.0 | |
| concepts[platform].gcmd_platform:not-provided | source · NASA CMR | connector:nasa_cmr@1.0.0 | |
| concepts[platform].gcmd_platform:ships | source · NASA CMR | connector:nasa_cmr@1.0.0 | |
| description | source · NASA CMR | connector:nasa_cmr@1.0.0 | /umm/Abstract |
| license_text | source · NASA CMR | connector:nasa_cmr@1.0.0 | |
| publication_date | source · NASA CMR | connector:nasa_cmr@1.0.0 | |
| spatial | source · NASA CMR | connector:nasa_cmr@1.0.0 | /umm/SpatialExtent |
| temporal | source · NASA CMR | connector:nasa_cmr@1.0.0 | /umm/TemporalExtents |
| title | source · NASA CMR | connector:nasa_cmr@1.0.0 | /umm/EntryTitle |
| version_label | source · NASA CMR | connector:nasa_cmr@1.0.0 |