DNA sequence data collected during the SIPEX II voyage of the Aurora Australis, 2012
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 br...
Other Authors: | , |
---|---|
Format: | Dataset |
Language: | unknown |
Published: |
Australian Ocean Data Network
|
Subjects: | |
Online Access: | https://researchdata.ands.org.au/dna-sequence-collected-australis-2012/685437 https://data.aad.gov.au/metadata/records/SIPEX_II_DNA_Sequences http://data.aad.gov.au/eds/3817/download https://secure3.aad.gov.au/proms/public/projects/report_project_public.cfm?project_no=4008 http://data.aad.gov.au/aadc/metadata/citation.cfm?entry_id=SIPEX_II_DNA_Sequences |
id |
ftands:oai:ands.org.au::685437 |
---|---|
record_format |
openpolar |
spelling |
ftands:oai:ands.org.au::685437 2023-05-15T13:46:55+02:00 DNA sequence data collected during the SIPEX II voyage of the Aurora Australis, 2012 AADC (originator) AU/AADC > Australian Antarctic Data Centre, Australia (resourceProvider) Spatial: northlimit=-42.0; southlimit=-66.0; westlimit=113.0; eastLimit=147.0 Temporal: From 2012-09-14 to 2012-11-16 https://researchdata.ands.org.au/dna-sequence-collected-australis-2012/685437 https://data.aad.gov.au/metadata/records/SIPEX_II_DNA_Sequences http://data.aad.gov.au/eds/3817/download https://secure3.aad.gov.au/proms/public/projects/report_project_public.cfm?project_no=4008 http://data.aad.gov.au/aadc/metadata/citation.cfm?entry_id=SIPEX_II_DNA_Sequences unknown Australian Ocean Data Network https://researchdata.ands.org.au/dna-sequence-collected-australis-2012/685437 c7b99575-9f8d-4249-a0fe-197b540ecfae https://data.aad.gov.au/metadata/records/SIPEX_II_DNA_Sequences http://data.aad.gov.au/eds/3817/download https://secure3.aad.gov.au/proms/public/projects/report_project_public.cfm?project_no=4008 http://data.aad.gov.au/aadc/metadata/citation.cfm?entry_id=SIPEX_II_DNA_Sequences https://data.aad.gov.au biota oceans BACTERIA/ARCHAEA EARTH SCIENCE BIOLOGICAL CLASSIFICATION 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 2020-01-05T21:06:21Z 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 16S rRNA reads in bacteria Phylum/Class and OTUs File: SCIPEXII_sea_ice_brines_eukaryote_community_OTU_data.xlsx contains information on the number of 16S rRNA reads in eukaryotic microbes: Phylum/Order/Closest taxon and OTUs Dataset Antarc* Antarctica aurora australis Sea ice Southern Ocean Research Data Australia (Australian National Data Service - ANDS) Lubbock ENVELOPE(169.133,169.133,-73.217,-73.217) Southern Ocean ENVELOPE(113.0,147.0,-42.0,-66.0) |
institution |
Open Polar |
collection |
Research Data Australia (Australian National Data Service - ANDS) |
op_collection_id |
ftands |
language |
unknown |
topic |
biota oceans BACTERIA/ARCHAEA EARTH SCIENCE BIOLOGICAL CLASSIFICATION 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 BACTERIA/ARCHAEA EARTH SCIENCE BIOLOGICAL CLASSIFICATION 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 BACTERIA/ARCHAEA EARTH SCIENCE BIOLOGICAL CLASSIFICATION 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 |
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 16S rRNA reads in bacteria Phylum/Class and OTUs File: SCIPEXII_sea_ice_brines_eukaryote_community_OTU_data.xlsx contains information on the number of 16S rRNA reads in eukaryotic microbes: Phylum/Order/Closest taxon and OTUs |
author2 |
AADC (originator) AU/AADC > Australian Antarctic Data Centre, Australia (resourceProvider) |
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.ands.org.au/dna-sequence-collected-australis-2012/685437 https://data.aad.gov.au/metadata/records/SIPEX_II_DNA_Sequences http://data.aad.gov.au/eds/3817/download https://secure3.aad.gov.au/proms/public/projects/report_project_public.cfm?project_no=4008 http://data.aad.gov.au/aadc/metadata/citation.cfm?entry_id=SIPEX_II_DNA_Sequences |
op_coverage |
Spatial: northlimit=-42.0; southlimit=-66.0; westlimit=113.0; eastLimit=147.0 Temporal: From 2012-09-14 to 2012-11-16 |
long_lat |
ENVELOPE(169.133,169.133,-73.217,-73.217) ENVELOPE(113.0,147.0,-42.0,-66.0) |
geographic |
Lubbock Southern Ocean |
geographic_facet |
Lubbock Southern Ocean |
genre |
Antarc* Antarctica aurora australis Sea ice Southern Ocean |
genre_facet |
Antarc* Antarctica aurora australis Sea ice Southern Ocean |
op_source |
https://data.aad.gov.au |
op_relation |
https://researchdata.ands.org.au/dna-sequence-collected-australis-2012/685437 c7b99575-9f8d-4249-a0fe-197b540ecfae https://data.aad.gov.au/metadata/records/SIPEX_II_DNA_Sequences http://data.aad.gov.au/eds/3817/download https://secure3.aad.gov.au/proms/public/projects/report_project_public.cfm?project_no=4008 http://data.aad.gov.au/aadc/metadata/citation.cfm?entry_id=SIPEX_II_DNA_Sequences |
_version_ |
1766245617255841792 |