DNA sequence data collected during the SIPEX II voyage of the Aurora Australis, 2012
Progress Code: completed Statement: A document detailing the methodology used is included in the dataset download. Purpose of experiments: Sequence data obtained to determine community structure of pack sea-ice microbial communities and whether it is effected by exposures to elevated CO2 levels. Sum...
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ftands:oai:ands.org.au::2820282 2024-09-15T17:42:30+00:00 DNA sequence data collected during the SIPEX II voyage of the Aurora Australis, 2012 AADC (owner) AADC, DATA OFFICER (distributor) AADC, DATA OFFICER (custodian) AU/AADC > Australian Antarctic Data Centre, Australia (hasAssociationWith) Australian Antarctic Data Centre (publisher) Australian Antarctic Division (sponsor) BOWMAN, JOHN (collaborator) BOWMAN, JOHN (hasPrincipalInvestigator) CONNELL, DAVE J. (author) MARTIN, ANDREW (collaborator) MARTIN, ANDREW (hasPrincipalInvestigator) MCMINN, ANDREW (hasPrincipalInvestigator) Martin, A., Bowman, J. and McMinn, A. (originator) Spatial: westlimit=113.0; southlimit=-66.0; eastlimit=147.0; northlimit=-42.0 Temporal: From 2012-09-14 to 2012-11-16 https://researchdata.edu.au/dna-sequence-collected-australis-2012/2820282 unknown Australian Ocean Data Network https://researchdata.edu.au/dna-sequence-collected-australis-2012/2820282 SIPEX_II_DNA_Sequences AU/AADC > Australian Antarctic Data Centre, Australia biota oceans EARTH SCIENCE > BIOLOGICAL CLASSIFICATION > BACTERIA/ARCHAEA Bacteria Eukaryotes DNA ADS > Automated DNA Sequencer SHIPS R/V AA > R/V Aurora Australis AMD/AU CEOS AMD ACE/CRC OCEAN > SOUTHERN OCEAN CONTINENT > ANTARCTICA GEOGRAPHIC REGION > POLAR dataset ftands 2024-08-06T01:58:58Z Progress Code: completed Statement: A document detailing the methodology used is included in the dataset download. Purpose of experiments: Sequence data obtained to determine community structure of pack sea-ice microbial communities and whether it is effected by exposures to elevated CO2 levels. Summary of Methods: Cells in sea-ice brines were filtered onto 0.2 micron filters and material extracted using the MoBio Water DNA extraction kit. The DNA was analysed by Research and Testing Laboratories Inc. (Lubbock, Texas, USA) via 454 pyrosequencing. The bacteria were analysed using primers set 10F-519R, which targets 16S rRNA genes. 16S rRNA genes associated with chloroplast and mitochondria are included in this dataset but represent a minority of sequences in most samples. Eukaryotes were analysed using primers set 550F-1055R, which targets 18S rRNA genes. The 454 pyrosequencing analysis with the Titanium GS FLX+ kit used generates on average 3000 reads incorporating custom pyrotags for later stages of the data analysis. The specific steps used for subsequent data analysis are described in the attached PDF file (Data_Analysis_Methodology.PDF). This output was further refined by first determining consensus sequences at the 98% similarity level using Weizhong Li’s online software site CD-HIT (http://weizhongli-lab.org/cd-hit/) Reference: Niu B, Fu L, Sun S, Li W. 2010. Artificial and natural duplicates in pyrosequencing reads of metagenomic data. BMC Bioinformatics 1:187 doi:10.1186/1471-2105-11-187. The consensus sequences were then checked for errors, manually curated, and aligned against closest matching sequences obtained from the NCBI database (www.ncbi.nlm.nih.gov) to finally obtained a list of consensus operational taxonomic entities and the number of reads obtained for each samples analysed. File: SIPEXII_DNA_Sample_information.xlsx provides sampling and analysis information for the detailed results in the other two files File: SCIPEXII__sea_ice_bacteria_OTUs.xlsx contains information on the number of ... Dataset Antarc* Antarctica aurora australis Sea ice Southern Ocean Research Data Australia (Australian National Data Service - ANDS) |
institution |
Open Polar |
collection |
Research Data Australia (Australian National Data Service - ANDS) |
op_collection_id |
ftands |
language |
unknown |
topic |
biota oceans EARTH SCIENCE > BIOLOGICAL CLASSIFICATION > BACTERIA/ARCHAEA Bacteria Eukaryotes DNA ADS > Automated DNA Sequencer SHIPS R/V AA > R/V Aurora Australis AMD/AU CEOS AMD ACE/CRC OCEAN > SOUTHERN OCEAN CONTINENT > ANTARCTICA GEOGRAPHIC REGION > POLAR |
spellingShingle |
biota oceans EARTH SCIENCE > BIOLOGICAL CLASSIFICATION > BACTERIA/ARCHAEA Bacteria Eukaryotes DNA ADS > Automated DNA Sequencer SHIPS R/V AA > R/V Aurora Australis AMD/AU CEOS AMD ACE/CRC OCEAN > SOUTHERN OCEAN CONTINENT > ANTARCTICA GEOGRAPHIC REGION > POLAR DNA sequence data collected during the SIPEX II voyage of the Aurora Australis, 2012 |
topic_facet |
biota oceans EARTH SCIENCE > BIOLOGICAL CLASSIFICATION > BACTERIA/ARCHAEA Bacteria Eukaryotes DNA ADS > Automated DNA Sequencer SHIPS R/V AA > R/V Aurora Australis AMD/AU CEOS AMD ACE/CRC OCEAN > SOUTHERN OCEAN CONTINENT > ANTARCTICA GEOGRAPHIC REGION > POLAR |
description |
Progress Code: completed Statement: A document detailing the methodology used is included in the dataset download. Purpose of experiments: Sequence data obtained to determine community structure of pack sea-ice microbial communities and whether it is effected by exposures to elevated CO2 levels. Summary of Methods: Cells in sea-ice brines were filtered onto 0.2 micron filters and material extracted using the MoBio Water DNA extraction kit. The DNA was analysed by Research and Testing Laboratories Inc. (Lubbock, Texas, USA) via 454 pyrosequencing. The bacteria were analysed using primers set 10F-519R, which targets 16S rRNA genes. 16S rRNA genes associated with chloroplast and mitochondria are included in this dataset but represent a minority of sequences in most samples. Eukaryotes were analysed using primers set 550F-1055R, which targets 18S rRNA genes. The 454 pyrosequencing analysis with the Titanium GS FLX+ kit used generates on average 3000 reads incorporating custom pyrotags for later stages of the data analysis. The specific steps used for subsequent data analysis are described in the attached PDF file (Data_Analysis_Methodology.PDF). This output was further refined by first determining consensus sequences at the 98% similarity level using Weizhong Li’s online software site CD-HIT (http://weizhongli-lab.org/cd-hit/) Reference: Niu B, Fu L, Sun S, Li W. 2010. Artificial and natural duplicates in pyrosequencing reads of metagenomic data. BMC Bioinformatics 1:187 doi:10.1186/1471-2105-11-187. The consensus sequences were then checked for errors, manually curated, and aligned against closest matching sequences obtained from the NCBI database (www.ncbi.nlm.nih.gov) to finally obtained a list of consensus operational taxonomic entities and the number of reads obtained for each samples analysed. File: SIPEXII_DNA_Sample_information.xlsx provides sampling and analysis information for the detailed results in the other two files File: SCIPEXII__sea_ice_bacteria_OTUs.xlsx contains information on the number of ... |
author2 |
AADC (owner) AADC, DATA OFFICER (distributor) AADC, DATA OFFICER (custodian) AU/AADC > Australian Antarctic Data Centre, Australia (hasAssociationWith) Australian Antarctic Data Centre (publisher) Australian Antarctic Division (sponsor) BOWMAN, JOHN (collaborator) BOWMAN, JOHN (hasPrincipalInvestigator) CONNELL, DAVE J. (author) MARTIN, ANDREW (collaborator) MARTIN, ANDREW (hasPrincipalInvestigator) MCMINN, ANDREW (hasPrincipalInvestigator) Martin, A., Bowman, J. and McMinn, A. (originator) |
format |
Dataset |
title |
DNA sequence data collected during the SIPEX II voyage of the Aurora Australis, 2012 |
title_short |
DNA sequence data collected during the SIPEX II voyage of the Aurora Australis, 2012 |
title_full |
DNA sequence data collected during the SIPEX II voyage of the Aurora Australis, 2012 |
title_fullStr |
DNA sequence data collected during the SIPEX II voyage of the Aurora Australis, 2012 |
title_full_unstemmed |
DNA sequence data collected during the SIPEX II voyage of the Aurora Australis, 2012 |
title_sort |
dna sequence data collected during the sipex ii voyage of the aurora australis, 2012 |
publisher |
Australian Ocean Data Network |
url |
https://researchdata.edu.au/dna-sequence-collected-australis-2012/2820282 |
op_coverage |
Spatial: westlimit=113.0; southlimit=-66.0; eastlimit=147.0; northlimit=-42.0 Temporal: From 2012-09-14 to 2012-11-16 |
genre |
Antarc* Antarctica aurora australis Sea ice Southern Ocean |
genre_facet |
Antarc* Antarctica aurora australis Sea ice Southern Ocean |
op_source |
AU/AADC > Australian Antarctic Data Centre, Australia |
op_relation |
https://researchdata.edu.au/dna-sequence-collected-australis-2012/2820282 SIPEX_II_DNA_Sequences |
_version_ |
1810489093666111488 |