Band pattern data from Desulfobacula-group specific DGGE for the SRE4 experiment
Samples are from the SRE4 experiment - an in situ experiment to determine fate and effects of different types of oils in the Antarctic marine environment. For details see: Powell S.M., Snape I., Bowman J.P., Thompson B.A.W., Stark J.S., McCammon S.A., Riddle M.J. 2005. A comparison of the short term...
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Australian Antarctic Data Centre
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Online Access: | https://researchdata.ands.org.au/band-pattern-desulfobacula-sre4-experiment/701812 https://doi.org/10.4225/15/55CC3E56211B6 https://data.aad.gov.au/metadata/records/SRE4_desulfobaculaDGGE http://nla.gov.au/nla.party-617536 |
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ftands:oai:ands.org.au::701812 |
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record_format |
openpolar |
institution |
Open Polar |
collection |
Research Data Australia (Australian National Data Service - ANDS) |
op_collection_id |
ftands |
language |
unknown |
topic |
environment CONTAMINANT LEVELS/SPILLS EARTH SCIENCE HUMAN DIMENSIONS ENVIRONMENTAL IMPACTS OIL SPILLS MARINE SEDIMENTS OCEANS BIODIVERSITY FUNCTIONS BIOSPHERE ECOLOGICAL DYNAMICS COMMUNITY DYNAMICS denaturing gradient gel electrophoresis microbial community structure oil contamination benthic microbiota Desfulfobacula ADS > Automated DNA Sequencer LABORATORY FIELD INVESTIGATION CONTINENT > ANTARCTICA > O'Brien Bay Windmill Islands GEOGRAPHIC REGION > POLAR |
spellingShingle |
environment CONTAMINANT LEVELS/SPILLS EARTH SCIENCE HUMAN DIMENSIONS ENVIRONMENTAL IMPACTS OIL SPILLS MARINE SEDIMENTS OCEANS BIODIVERSITY FUNCTIONS BIOSPHERE ECOLOGICAL DYNAMICS COMMUNITY DYNAMICS denaturing gradient gel electrophoresis microbial community structure oil contamination benthic microbiota Desfulfobacula ADS > Automated DNA Sequencer LABORATORY FIELD INVESTIGATION CONTINENT > ANTARCTICA > O'Brien Bay Windmill Islands GEOGRAPHIC REGION > POLAR Band pattern data from Desulfobacula-group specific DGGE for the SRE4 experiment |
topic_facet |
environment CONTAMINANT LEVELS/SPILLS EARTH SCIENCE HUMAN DIMENSIONS ENVIRONMENTAL IMPACTS OIL SPILLS MARINE SEDIMENTS OCEANS BIODIVERSITY FUNCTIONS BIOSPHERE ECOLOGICAL DYNAMICS COMMUNITY DYNAMICS denaturing gradient gel electrophoresis microbial community structure oil contamination benthic microbiota Desfulfobacula ADS > Automated DNA Sequencer LABORATORY FIELD INVESTIGATION CONTINENT > ANTARCTICA > O'Brien Bay Windmill Islands GEOGRAPHIC REGION > POLAR |
description |
Samples are from the SRE4 experiment - an in situ experiment to determine fate and effects of different types of oils in the Antarctic marine environment. For details see: Powell S.M., Snape I., Bowman J.P., Thompson B.A.W., Stark J.S., McCammon S.A., Riddle M.J. 2005. A comparison of the short term effects of diesel fuel and lubricant oils on Antarctic benthic microbial communities. Journal of Experimental Marine Biology and Ecology 322:53-65. Samples were analysed by denaturing gradient gel electrophoresis (DGGE) with primers specific for the Desulfobacula group. Samples A,B,C,D,E,F,G,H,I are all initial samples collected different days Samples beginning T0 are predeployment samples, the next number refers to the batch. Samples beginning T2 are 1 year samples with: C = control S = SAB L = lubricant U = used lubricant B = biodegradable lubricant PCR conditions were as follows: Primers: 764F: ACAATGGTAAATGAGGGCA 1392RC: CGCCCGCCGCGCCCCGCGCCCGGCCCGCCGCCCCCGCCCCACGGGCGG TGTGTAC 50 ul (micro litre) reactions with Advantage II taq (Clontech) following manufacturer's recommendations with 20 pmol (pico mol) each primer and 20 ng (nano gram) template DNA. Cycling: 94C 5 minutes 10 cycles of: 94C 1 minutes 65C 1 minutes (-1C per cycle) 72C 2 minutes 20 cycles of: 94C 1 minutes 55C 1 minutes 72C 2 minutes 72C 30 minutes DGGE carried out using the D-Code system (BioRad). Gel: 8% acrylamide 30 - 65% denaturant with 2 cm stacking gel (15% acrylamide) 1 x TAE, 60 degrees C, 70V 16 hours The gels were pre-run for 20 minutes then half reaction volume was loaded and the lanes flushed out after 15 minutes. Gels were stained with SYBRGold. Images were captured using Storm Phosphorimager and ImageQuant v5.2 software(.gel files). Samples were only compared within a gel. Band pattern results are in the file desulfodgge.xls. For each comparison made there is a separate sheet in this file (see below). The first column in each sheet is the band position (or band name) and the remaining columns are samples with the first row being the sample name. '0' '1' indicate the band was 'absent' or 'present'. Comparison Image files (.gel and .tif) results sheets Background variation 140704f; 140704b 140704f and 140704b predeployment batches 180604f; 180406b 180604f and 180604b effect of setup 150704 150704 immediate effect of oil 250604f; 250604b 250604f and 250604b 1 year samples (T2) 040804f; 040804b 040804f and 040804b This work was completed as part of ASAC projects 1228 and 2201 (ASAC_1228, ASAC_2201). |
author2 |
BOWMAN, JOHN (hasPrincipalInvestigator) POWELL, SHANE (hasPrincipalInvestigator) POWELL, SHANE (processor) RIDDLE, MARTIN J. (hasPrincipalInvestigator) Australian Antarctic Data Centre (publisher) |
format |
Dataset |
title |
Band pattern data from Desulfobacula-group specific DGGE for the SRE4 experiment |
title_short |
Band pattern data from Desulfobacula-group specific DGGE for the SRE4 experiment |
title_full |
Band pattern data from Desulfobacula-group specific DGGE for the SRE4 experiment |
title_fullStr |
Band pattern data from Desulfobacula-group specific DGGE for the SRE4 experiment |
title_full_unstemmed |
Band pattern data from Desulfobacula-group specific DGGE for the SRE4 experiment |
title_sort |
band pattern data from desulfobacula-group specific dgge for the sre4 experiment |
publisher |
Australian Antarctic Data Centre |
url |
https://researchdata.ands.org.au/band-pattern-desulfobacula-sre4-experiment/701812 https://doi.org/10.4225/15/55CC3E56211B6 https://data.aad.gov.au/metadata/records/SRE4_desulfobaculaDGGE http://nla.gov.au/nla.party-617536 |
op_coverage |
Spatial: northlimit=-66; southlimit=-67; westlimit=110; eastLimit=111; projection=WGS84 Temporal: From 2001-10-25 to 2003-03-30 |
long_lat |
ENVELOPE(110.417,110.417,-66.350,-66.350) ENVELOPE(18.933,18.933,69.617,69.617) ENVELOPE(110.524,110.524,-66.302,-66.302) ENVELOPE(110,111,-66,-67) |
geographic |
Antarctic The Antarctic Windmill Islands Lanes O'Brien Bay |
geographic_facet |
Antarctic The Antarctic Windmill Islands Lanes O'Brien Bay |
genre |
Antarc* Antarctic Antarctica Windmill Islands |
genre_facet |
Antarc* Antarctic Antarctica Windmill Islands |
op_source |
Australian Antarctic Data Centre |
op_relation |
https://researchdata.ands.org.au/band-pattern-desulfobacula-sre4-experiment/701812 cfe6fc0c-324d-4fa3-a09a-f7caf2c63b3c doi:10.4225/15/55CC3E56211B6 SRE4_desulfobaculaDGGE https://data.aad.gov.au/metadata/records/SRE4_desulfobaculaDGGE http://nla.gov.au/nla.party-617536 |
op_doi |
https://doi.org/10.4225/15/55CC3E56211B6 |
_version_ |
1766246102413082624 |
spelling |
ftands:oai:ands.org.au::701812 2023-05-15T13:46:59+02:00 Band pattern data from Desulfobacula-group specific DGGE for the SRE4 experiment BOWMAN, JOHN (hasPrincipalInvestigator) POWELL, SHANE (hasPrincipalInvestigator) POWELL, SHANE (processor) RIDDLE, MARTIN J. (hasPrincipalInvestigator) Australian Antarctic Data Centre (publisher) Spatial: northlimit=-66; southlimit=-67; westlimit=110; eastLimit=111; projection=WGS84 Temporal: From 2001-10-25 to 2003-03-30 https://researchdata.ands.org.au/band-pattern-desulfobacula-sre4-experiment/701812 https://doi.org/10.4225/15/55CC3E56211B6 https://data.aad.gov.au/metadata/records/SRE4_desulfobaculaDGGE http://nla.gov.au/nla.party-617536 unknown Australian Antarctic Data Centre https://researchdata.ands.org.au/band-pattern-desulfobacula-sre4-experiment/701812 cfe6fc0c-324d-4fa3-a09a-f7caf2c63b3c doi:10.4225/15/55CC3E56211B6 SRE4_desulfobaculaDGGE https://data.aad.gov.au/metadata/records/SRE4_desulfobaculaDGGE http://nla.gov.au/nla.party-617536 Australian Antarctic Data Centre environment CONTAMINANT LEVELS/SPILLS EARTH SCIENCE HUMAN DIMENSIONS ENVIRONMENTAL IMPACTS OIL SPILLS MARINE SEDIMENTS OCEANS BIODIVERSITY FUNCTIONS BIOSPHERE ECOLOGICAL DYNAMICS COMMUNITY DYNAMICS denaturing gradient gel electrophoresis microbial community structure oil contamination benthic microbiota Desfulfobacula ADS > Automated DNA Sequencer LABORATORY FIELD INVESTIGATION CONTINENT > ANTARCTICA > O'Brien Bay Windmill Islands GEOGRAPHIC REGION > POLAR dataset ftands https://doi.org/10.4225/15/55CC3E56211B6 2020-01-05T21:19:19Z Samples are from the SRE4 experiment - an in situ experiment to determine fate and effects of different types of oils in the Antarctic marine environment. For details see: Powell S.M., Snape I., Bowman J.P., Thompson B.A.W., Stark J.S., McCammon S.A., Riddle M.J. 2005. A comparison of the short term effects of diesel fuel and lubricant oils on Antarctic benthic microbial communities. Journal of Experimental Marine Biology and Ecology 322:53-65. Samples were analysed by denaturing gradient gel electrophoresis (DGGE) with primers specific for the Desulfobacula group. Samples A,B,C,D,E,F,G,H,I are all initial samples collected different days Samples beginning T0 are predeployment samples, the next number refers to the batch. Samples beginning T2 are 1 year samples with: C = control S = SAB L = lubricant U = used lubricant B = biodegradable lubricant PCR conditions were as follows: Primers: 764F: ACAATGGTAAATGAGGGCA 1392RC: CGCCCGCCGCGCCCCGCGCCCGGCCCGCCGCCCCCGCCCCACGGGCGG TGTGTAC 50 ul (micro litre) reactions with Advantage II taq (Clontech) following manufacturer's recommendations with 20 pmol (pico mol) each primer and 20 ng (nano gram) template DNA. Cycling: 94C 5 minutes 10 cycles of: 94C 1 minutes 65C 1 minutes (-1C per cycle) 72C 2 minutes 20 cycles of: 94C 1 minutes 55C 1 minutes 72C 2 minutes 72C 30 minutes DGGE carried out using the D-Code system (BioRad). Gel: 8% acrylamide 30 - 65% denaturant with 2 cm stacking gel (15% acrylamide) 1 x TAE, 60 degrees C, 70V 16 hours The gels were pre-run for 20 minutes then half reaction volume was loaded and the lanes flushed out after 15 minutes. Gels were stained with SYBRGold. Images were captured using Storm Phosphorimager and ImageQuant v5.2 software(.gel files). Samples were only compared within a gel. Band pattern results are in the file desulfodgge.xls. For each comparison made there is a separate sheet in this file (see below). The first column in each sheet is the band position (or band name) and the remaining columns are samples with the first row being the sample name. '0' '1' indicate the band was 'absent' or 'present'. Comparison Image files (.gel and .tif) results sheets Background variation 140704f; 140704b 140704f and 140704b predeployment batches 180604f; 180406b 180604f and 180604b effect of setup 150704 150704 immediate effect of oil 250604f; 250604b 250604f and 250604b 1 year samples (T2) 040804f; 040804b 040804f and 040804b This work was completed as part of ASAC projects 1228 and 2201 (ASAC_1228, ASAC_2201). Dataset Antarc* Antarctic Antarctica Windmill Islands Research Data Australia (Australian National Data Service - ANDS) Antarctic The Antarctic Windmill Islands ENVELOPE(110.417,110.417,-66.350,-66.350) Lanes ENVELOPE(18.933,18.933,69.617,69.617) O'Brien Bay ENVELOPE(110.524,110.524,-66.302,-66.302) ENVELOPE(110,111,-66,-67) |