Data · collection · 2018
Short Tailed Shearwater DREAM gene sequencing fastq files
Listed in NASA Earthdata CMR
This data set includes unprocessed sample .fastq files from two separate Illumina NextSeq runs, labelled as 'Run_1' and 'Run_2', respectively.
Description
Sample names: e.g. STS15059, 'STS' is the abbreviation of Short-tailed shearwater. The first two digits of the numeric refer to the year of collection e.g. '15' = 2015.
Finally, the following number refers to the sequential unique ID for that year, e.g. '059' is the fifty-ninth sample for the years' collection. Leg bands are also recorded and are generally a 5-digit number and are unique to the individual bird. Longitudinal samples can be identified using these band IDs.
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E.g. in Run_2, an individual with the band number: 52196, was collected in 2015 as 'STS15065' and again in 2017 as 'STS17044'. Run_1: N = 35 individual samples are split across 4 lanes e.g. 'STS16020_S35_L001(/L002/L003/L004)_R1_001/fastq' and need to be merged before conversion to .fasta format and downstream analysis. Run_2: N = 36 individual samples were provided as a single merged file from the service provider, e.g. 'STS15059_S34_R1_001.fastq'.
Sample_info: This excel spreadsheet has information on samples as follows: 'Band': 5-digit number on leg band. 'Sample': Sample number within run. 'UID': The unique ID for collection year e.g. STS15007. 'Age': The known-age of the animal rounded to whole year. 'Index (NebNext)': The NEB index used for NGS sample identification. 'Note': Additional information on if a sample was a between or within run replicate or longitudinal replicate.
Analysis of these data will be published in: [tba: R. De Paoli-Iseppi et al. 2018. Molecular Ecology Resources].
Links
Get the data
- Request a copy of the data data.aad.gov.au/eds/4791/download ↗
download · from NASA CMR
Where it is published
- DOI doi.org/10.26179/5bd28a9be61d9 ↗
DOI / persistent id · from NASA CMR
Documentation and papers
- data.aad.gov.au /aadc/metadata/citation.cfm?entry_id=AAS_4014_shearwater_DREAM ↗
Citation reference for this metadata record and dataset.
documentation · from NASA CMR
- Public information for AAS project AAS_4014 secure3.aad.gov.au/proms/public/projects/report_project_public.cfm?project_no=AAS… ↗
project · from NASA CMR
Catalogue records · 2
- CMR UMM-JSON cmr.earthdata.nasa.gov/search/concepts/C1565992326-AU_AADC.umm_json ↗
metadata API · from NASA CMR
- CMR record cmr.earthdata.nasa.gov/search/concepts/C1565992326-AU_AADC.html ↗
catalogue entry · from NASA CMR
Topics
- Stated by source
- Albatrosses/Petrels And Allies · Automated DNA Sequencer · LABORATORY
- Inferred from text
- Longitudinal study 65% · Sequencing 75%
Provenance · 1 source records, 13 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| NASA Earthdata CMR | C1565992326-AU_AADC | 8 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-vertebrates/birds/albatrosses-petrels-and-allies | source · NASA CMR | connector:nasa_cmr@1.0.0 | |
| concepts[method].local:method:longitudinal-study | enrichment · NASA CMR | keyword-concept-rules@1.0.0 | title+description (65%) |
| concepts[modality].local:modality:sequencing | enrichment · NASA CMR | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[platform].gcmd_platform:laboratory | 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 |