Genetic identification of fish caught as bycatch in the Antarctic krill fishery and comparison with observer records
Progress Code: completed Statement: The values provided in temporal coverage are approximate only and correspond to rough dates for the project as a whole. 1st Experiment 24/11/16 ************************************************************************************************ See 2016_11_24_Miseq_Sh...
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ftands:oai:ands.org.au::2823012 2023-10-09T21:46:54+02:00 Genetic identification of fish caught as bycatch in the Antarctic krill fishery and comparison with observer records Spatial: westlimit=50; southlimit=-65; eastlimit=150; northlimit=-55 Temporal: From 2014-07-01 to 2018-06-30 https://researchdata.edu.au/genetic-identification-fish-observer-records/2823012 unknown Australian Ocean Data Network https://researchdata.edu.au/genetic-identification-fish-observer-records/2823012 AAS_4313_Larval_Fish_Bycatch_ID Dataset DOI AU/AADC > Australian Antarctic Data Centre, Australia biota oceans EARTH SCIENCE > OCEANS > AQUATIC SCIENCES > FISHERIES BIOLOGICAL CLASSIFICATION > ANIMALS/INVERTEBRATES > ARTHROPODS > CRUSTACEANS > EUPHAUSIIDS (KRILL) BIOSPHERE > ECOLOGICAL DYNAMICS > SPECIES/POPULATION INTERACTIONS > SPECIES LIFE HISTORY GENETICS GENETIC IDENTIFICATION DNA ADS > Automated DNA Sequencer TRAWL LABORATORY SHIPS AMD AMD/AU CEOS GEOGRAPHIC REGION > POLAR OCEAN > SOUTHERN OCEAN CONTINENT > ANTARCTICA dataset ftands 2023-09-18T22:50:25Z Progress Code: completed Statement: The values provided in temporal coverage are approximate only and correspond to rough dates for the project as a whole. 1st Experiment 24/11/16 ************************************************************************************************ See 2016_11_24_Miseq_Sheet 1. Sanger Sequencing Plate #4 - 25mg of Tissue was extracted by AGRF. DNA was diluted to 5ng/ul. Samples were sanger sequenced with 16SAR (Palumbi) primer. If they failed, I used COI3 cocktail (Ivanova). FASTA sequences from Plate 4 are in the folder named Sanger Sequence FASTA Plate #4. Naming - Plate position, primer, sample ID. ie reater than A1-16S-AR_1952. 2. DNA and Tissue Pools of Plate 4 We wanted to explore the possibility of using a metabarcoding approach. For metabarcoding we re-examined specimens already identified from sanger sequences. We mixed DNA from many samples (n=16 or n=96) and did a single amplification (i.e. up to 96 DNA extractions processed in a single-tube marker amplification). We also took it a step further and tried blending a set amount of tissue from many fish specimens (n=16 or n=96) and did a single DNA extraction on the tissue mixes (i.e. a single DNA extraction and single tube amplification for up to 96 samples). See 2016_11_24_Miseq_Sheet for DNA and Tissue Pool mixes. 3. Miseq Run 16 samples were ran on a 250bp pe read. Each sample was amplified with 3 primer sets - COI (please note one dual labelled set was used), 12s and 16s (Primers listed on 2016_11_24_Miseq_Sheet). They were diluted 1:10 and illumina sequencing adaptors were added (please note I used same I7 and I5 per sample, so they had to be sorted on amplicon). 2016_11_24_fastq_files has the data from miseq. and 2016_11_24_merged_fastq_files has the merged files. For some unknown reason 16s tissue produced no data. 2nd Experiment 04/07/17 ************************************************************************************************* 1. DNA Extractions Plate #1, 2 and 3 - 25mg of Tisse was extracted by AGRF. DNA ... Dataset Antarc* Antarctic Antarctic Krill Antarctica Southern Ocean Research Data Australia (Australian National Data Service - ANDS) Antarctic Southern Ocean The Antarctic Ivanova ENVELOPE(65.450,65.450,-70.167,-70.167) |
institution |
Open Polar |
collection |
Research Data Australia (Australian National Data Service - ANDS) |
op_collection_id |
ftands |
language |
unknown |
topic |
biota oceans EARTH SCIENCE > OCEANS > AQUATIC SCIENCES > FISHERIES BIOLOGICAL CLASSIFICATION > ANIMALS/INVERTEBRATES > ARTHROPODS > CRUSTACEANS > EUPHAUSIIDS (KRILL) BIOSPHERE > ECOLOGICAL DYNAMICS > SPECIES/POPULATION INTERACTIONS > SPECIES LIFE HISTORY GENETICS GENETIC IDENTIFICATION DNA ADS > Automated DNA Sequencer TRAWL LABORATORY SHIPS AMD AMD/AU CEOS GEOGRAPHIC REGION > POLAR OCEAN > SOUTHERN OCEAN CONTINENT > ANTARCTICA |
spellingShingle |
biota oceans EARTH SCIENCE > OCEANS > AQUATIC SCIENCES > FISHERIES BIOLOGICAL CLASSIFICATION > ANIMALS/INVERTEBRATES > ARTHROPODS > CRUSTACEANS > EUPHAUSIIDS (KRILL) BIOSPHERE > ECOLOGICAL DYNAMICS > SPECIES/POPULATION INTERACTIONS > SPECIES LIFE HISTORY GENETICS GENETIC IDENTIFICATION DNA ADS > Automated DNA Sequencer TRAWL LABORATORY SHIPS AMD AMD/AU CEOS GEOGRAPHIC REGION > POLAR OCEAN > SOUTHERN OCEAN CONTINENT > ANTARCTICA Genetic identification of fish caught as bycatch in the Antarctic krill fishery and comparison with observer records |
topic_facet |
biota oceans EARTH SCIENCE > OCEANS > AQUATIC SCIENCES > FISHERIES BIOLOGICAL CLASSIFICATION > ANIMALS/INVERTEBRATES > ARTHROPODS > CRUSTACEANS > EUPHAUSIIDS (KRILL) BIOSPHERE > ECOLOGICAL DYNAMICS > SPECIES/POPULATION INTERACTIONS > SPECIES LIFE HISTORY GENETICS GENETIC IDENTIFICATION DNA ADS > Automated DNA Sequencer TRAWL LABORATORY SHIPS AMD AMD/AU CEOS GEOGRAPHIC REGION > POLAR OCEAN > SOUTHERN OCEAN CONTINENT > ANTARCTICA |
description |
Progress Code: completed Statement: The values provided in temporal coverage are approximate only and correspond to rough dates for the project as a whole. 1st Experiment 24/11/16 ************************************************************************************************ See 2016_11_24_Miseq_Sheet 1. Sanger Sequencing Plate #4 - 25mg of Tissue was extracted by AGRF. DNA was diluted to 5ng/ul. Samples were sanger sequenced with 16SAR (Palumbi) primer. If they failed, I used COI3 cocktail (Ivanova). FASTA sequences from Plate 4 are in the folder named Sanger Sequence FASTA Plate #4. Naming - Plate position, primer, sample ID. ie reater than A1-16S-AR_1952. 2. DNA and Tissue Pools of Plate 4 We wanted to explore the possibility of using a metabarcoding approach. For metabarcoding we re-examined specimens already identified from sanger sequences. We mixed DNA from many samples (n=16 or n=96) and did a single amplification (i.e. up to 96 DNA extractions processed in a single-tube marker amplification). We also took it a step further and tried blending a set amount of tissue from many fish specimens (n=16 or n=96) and did a single DNA extraction on the tissue mixes (i.e. a single DNA extraction and single tube amplification for up to 96 samples). See 2016_11_24_Miseq_Sheet for DNA and Tissue Pool mixes. 3. Miseq Run 16 samples were ran on a 250bp pe read. Each sample was amplified with 3 primer sets - COI (please note one dual labelled set was used), 12s and 16s (Primers listed on 2016_11_24_Miseq_Sheet). They were diluted 1:10 and illumina sequencing adaptors were added (please note I used same I7 and I5 per sample, so they had to be sorted on amplicon). 2016_11_24_fastq_files has the data from miseq. and 2016_11_24_merged_fastq_files has the merged files. For some unknown reason 16s tissue produced no data. 2nd Experiment 04/07/17 ************************************************************************************************* 1. DNA Extractions Plate #1, 2 and 3 - 25mg of Tisse was extracted by AGRF. DNA ... |
format |
Dataset |
title |
Genetic identification of fish caught as bycatch in the Antarctic krill fishery and comparison with observer records |
title_short |
Genetic identification of fish caught as bycatch in the Antarctic krill fishery and comparison with observer records |
title_full |
Genetic identification of fish caught as bycatch in the Antarctic krill fishery and comparison with observer records |
title_fullStr |
Genetic identification of fish caught as bycatch in the Antarctic krill fishery and comparison with observer records |
title_full_unstemmed |
Genetic identification of fish caught as bycatch in the Antarctic krill fishery and comparison with observer records |
title_sort |
genetic identification of fish caught as bycatch in the antarctic krill fishery and comparison with observer records |
publisher |
Australian Ocean Data Network |
url |
https://researchdata.edu.au/genetic-identification-fish-observer-records/2823012 |
op_coverage |
Spatial: westlimit=50; southlimit=-65; eastlimit=150; northlimit=-55 Temporal: From 2014-07-01 to 2018-06-30 |
long_lat |
ENVELOPE(65.450,65.450,-70.167,-70.167) |
geographic |
Antarctic Southern Ocean The Antarctic Ivanova |
geographic_facet |
Antarctic Southern Ocean The Antarctic Ivanova |
genre |
Antarc* Antarctic Antarctic Krill Antarctica Southern Ocean |
genre_facet |
Antarc* Antarctic Antarctic Krill Antarctica Southern Ocean |
op_source |
AU/AADC > Australian Antarctic Data Centre, Australia |
op_relation |
https://researchdata.edu.au/genetic-identification-fish-observer-records/2823012 AAS_4313_Larval_Fish_Bycatch_ID Dataset DOI |
_version_ |
1779309508470767616 |