Microfluidic quantitative PCR data for in-situ Macquarie Island Mesocosm assessing the toxicity of residual hydrocarbons.
This data set is the product of three high-throughput qPCR dynamic array Fluidigm chips. Data is semi-processed, as Fluidigm software does not allow the export of raw fluorescence data. In-situ soil mesocosms (n=20) were set up on Macquarie Island in February 2013. Following a year's equilibrat...
Other Authors: | , , , , , , , , , |
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Format: | Dataset |
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Australian Antarctic Data Centre
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Online Access: | https://researchdata.ands.org.au/microfluidic-quantitative-pcr-residual-hydrocarbons/699128 https://doi.org/10.4225/15/57622D1CB886D https://data.aad.gov.au/metadata/records/AAS_4135_Hydrocarbon_Toxicity http://nla.gov.au/nla.party-617536 |
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ftands:oai:ands.org.au::699128 |
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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 EARTH SCIENCE > TERRESTRIAL HYDROSPHERE > WATER QUALITY/WATER CHEMISTRY > CONTAMINANTS > PETROLEUM HYDROCARBONS CONTAMINANT LEVELS/SPILLS EARTH SCIENCE HUMAN DIMENSIONS ENVIRONMENTAL IMPACTS DNA SOIL ADS > Automated DNA Sequencer FIELD INVESTIGATION FIELD SURVEYS GEOGRAPHIC REGION > POLAR OCEAN > SOUTHERN OCEAN > MACQUARIE ISLAND |
spellingShingle |
environment EARTH SCIENCE > TERRESTRIAL HYDROSPHERE > WATER QUALITY/WATER CHEMISTRY > CONTAMINANTS > PETROLEUM HYDROCARBONS CONTAMINANT LEVELS/SPILLS EARTH SCIENCE HUMAN DIMENSIONS ENVIRONMENTAL IMPACTS DNA SOIL ADS > Automated DNA Sequencer FIELD INVESTIGATION FIELD SURVEYS GEOGRAPHIC REGION > POLAR OCEAN > SOUTHERN OCEAN > MACQUARIE ISLAND Microfluidic quantitative PCR data for in-situ Macquarie Island Mesocosm assessing the toxicity of residual hydrocarbons. |
topic_facet |
environment EARTH SCIENCE > TERRESTRIAL HYDROSPHERE > WATER QUALITY/WATER CHEMISTRY > CONTAMINANTS > PETROLEUM HYDROCARBONS CONTAMINANT LEVELS/SPILLS EARTH SCIENCE HUMAN DIMENSIONS ENVIRONMENTAL IMPACTS DNA SOIL ADS > Automated DNA Sequencer FIELD INVESTIGATION FIELD SURVEYS GEOGRAPHIC REGION > POLAR OCEAN > SOUTHERN OCEAN > MACQUARIE ISLAND |
description |
This data set is the product of three high-throughput qPCR dynamic array Fluidigm chips. Data is semi-processed, as Fluidigm software does not allow the export of raw fluorescence data. In-situ soil mesocosms (n=20) were set up on Macquarie Island in February 2013. Following a year's equilibration, mesocosms were spiked in triplicate with a fuel mixture mimicking the composition of aged fuel spills on Macquarie Island, in addition to five solvent-only controls. Spiking concentrations range from 50mg/kg to 10000 mg/kg, all in triplicate, in addition to 5 solvent - only controls. Soils have been sampled from initial set up until April 2015, with a total of 2 pre-spike and 4 post-spike sample sets. DNA was extracted from soil in triplicate. Automated Ribosomal Intergenic Spacer analysis (ARISA) was conducted for both Fungal and Bacterial soil communities across all extractions (n = 270). ARISA results confirmed uniformity of replicate extractions. One replicate for each sample was selected for further work (n=90). Microfluidic qPCR was conducted with the 90 samples and assays for 16 different genes, 14 of which worked. See Thesis in publications section for more details. First dataset is the semi-processed data output from Fluidigm program (it does not allow the export of un-processed data). Consult Fluidigm Real-Time PCR Analysis User Guide (PN 68000088 J1) for more information on columns A-N (ID, Type, relative Conc, Value, Calibrated rConc, Quality, Threshold, In Range, Out Range, Peak Ratio). Assay = gene assayed, see Thesis in publication for more details. Name = sample name and individual extraction replicate; A,B,or C. Plate = individual Fluidigm chip; three were run, 90, 91 and 92. Time refers to sample set, see Question 2. Treatment = nominal spiking concentration of mesocosm. Dilution factor = dilution factor of sample prior to submission for microfluidic qPCR. Copies/ ul = gene copy number of DNA sample. Initial volume = extraction volume. G of soil = weight of soil extracted. Comb_cond is purely for ease of processing with factor qPCR. Factor qPCR corrected copies/g = output once interpolate differences were corrected with factor qPCR. Processed gene copy number data (copies/g) is provided in second spreadsheet in 'Biological'. 'Environmental' tab provides additional data on samples, including TPH data and vegetation observations at one time point (expressed as percentage of coverage). Contact Sarah Houlahan for more information on chemical data. |
author2 |
CRANE, SALLY L. (hasPrincipalInvestigator) CRANE, SALLY L. (processor) FERRARI, BELINDA C (hasPrincipalInvestigator) FERRARI, BELINDA C (processor) HOSE, GRANT (hasPrincipalInvestigator) ERRINGTON, INGRID (processor) GEORGE, SIMON CHRISTOPHER (processor) HOULAHAN, SARAH (processor) KING, CATHERINE K. (processor) Australian Antarctic Data Centre (publisher) |
format |
Dataset |
title |
Microfluidic quantitative PCR data for in-situ Macquarie Island Mesocosm assessing the toxicity of residual hydrocarbons. |
title_short |
Microfluidic quantitative PCR data for in-situ Macquarie Island Mesocosm assessing the toxicity of residual hydrocarbons. |
title_full |
Microfluidic quantitative PCR data for in-situ Macquarie Island Mesocosm assessing the toxicity of residual hydrocarbons. |
title_fullStr |
Microfluidic quantitative PCR data for in-situ Macquarie Island Mesocosm assessing the toxicity of residual hydrocarbons. |
title_full_unstemmed |
Microfluidic quantitative PCR data for in-situ Macquarie Island Mesocosm assessing the toxicity of residual hydrocarbons. |
title_sort |
microfluidic quantitative pcr data for in-situ macquarie island mesocosm assessing the toxicity of residual hydrocarbons. |
publisher |
Australian Antarctic Data Centre |
url |
https://researchdata.ands.org.au/microfluidic-quantitative-pcr-residual-hydrocarbons/699128 https://doi.org/10.4225/15/57622D1CB886D https://data.aad.gov.au/metadata/records/AAS_4135_Hydrocarbon_Toxicity http://nla.gov.au/nla.party-617536 |
op_coverage |
Spatial: northlimit=-54.4990; southlimit=-54.4991; westlimit=158.9391; eastLimit=158.9393; projection=WGS84 Temporal: From 2013-01-17 to 2015-03-24 |
long_lat |
ENVELOPE(158.9391,158.9393,-54.4990,-54.4991) |
geographic |
Southern Ocean |
geographic_facet |
Southern Ocean |
genre |
Macquarie Island Southern Ocean |
genre_facet |
Macquarie Island Southern Ocean |
op_source |
Australian Antarctic Data Centre |
op_relation |
https://researchdata.ands.org.au/microfluidic-quantitative-pcr-residual-hydrocarbons/699128 b1da8245-7bae-4984-903b-fafbbdea97f4 doi:10.4225/15/57622D1CB886D AAS_4135_Hydrocarbon_Toxicity https://data.aad.gov.au/metadata/records/AAS_4135_Hydrocarbon_Toxicity http://nla.gov.au/nla.party-617536 |
op_doi |
https://doi.org/10.4225/15/57622D1CB886D |
_version_ |
1766066300773203968 |
spelling |
ftands:oai:ands.org.au::699128 2023-05-15T17:09:56+02:00 Microfluidic quantitative PCR data for in-situ Macquarie Island Mesocosm assessing the toxicity of residual hydrocarbons. CRANE, SALLY L. (hasPrincipalInvestigator) CRANE, SALLY L. (processor) FERRARI, BELINDA C (hasPrincipalInvestigator) FERRARI, BELINDA C (processor) HOSE, GRANT (hasPrincipalInvestigator) ERRINGTON, INGRID (processor) GEORGE, SIMON CHRISTOPHER (processor) HOULAHAN, SARAH (processor) KING, CATHERINE K. (processor) Australian Antarctic Data Centre (publisher) Spatial: northlimit=-54.4990; southlimit=-54.4991; westlimit=158.9391; eastLimit=158.9393; projection=WGS84 Temporal: From 2013-01-17 to 2015-03-24 https://researchdata.ands.org.au/microfluidic-quantitative-pcr-residual-hydrocarbons/699128 https://doi.org/10.4225/15/57622D1CB886D https://data.aad.gov.au/metadata/records/AAS_4135_Hydrocarbon_Toxicity http://nla.gov.au/nla.party-617536 unknown Australian Antarctic Data Centre https://researchdata.ands.org.au/microfluidic-quantitative-pcr-residual-hydrocarbons/699128 b1da8245-7bae-4984-903b-fafbbdea97f4 doi:10.4225/15/57622D1CB886D AAS_4135_Hydrocarbon_Toxicity https://data.aad.gov.au/metadata/records/AAS_4135_Hydrocarbon_Toxicity http://nla.gov.au/nla.party-617536 Australian Antarctic Data Centre environment EARTH SCIENCE > TERRESTRIAL HYDROSPHERE > WATER QUALITY/WATER CHEMISTRY > CONTAMINANTS > PETROLEUM HYDROCARBONS CONTAMINANT LEVELS/SPILLS EARTH SCIENCE HUMAN DIMENSIONS ENVIRONMENTAL IMPACTS DNA SOIL ADS > Automated DNA Sequencer FIELD INVESTIGATION FIELD SURVEYS GEOGRAPHIC REGION > POLAR OCEAN > SOUTHERN OCEAN > MACQUARIE ISLAND dataset ftands https://doi.org/10.4225/15/57622D1CB886D 2020-01-05T21:15:47Z This data set is the product of three high-throughput qPCR dynamic array Fluidigm chips. Data is semi-processed, as Fluidigm software does not allow the export of raw fluorescence data. In-situ soil mesocosms (n=20) were set up on Macquarie Island in February 2013. Following a year's equilibration, mesocosms were spiked in triplicate with a fuel mixture mimicking the composition of aged fuel spills on Macquarie Island, in addition to five solvent-only controls. Spiking concentrations range from 50mg/kg to 10000 mg/kg, all in triplicate, in addition to 5 solvent - only controls. Soils have been sampled from initial set up until April 2015, with a total of 2 pre-spike and 4 post-spike sample sets. DNA was extracted from soil in triplicate. Automated Ribosomal Intergenic Spacer analysis (ARISA) was conducted for both Fungal and Bacterial soil communities across all extractions (n = 270). ARISA results confirmed uniformity of replicate extractions. One replicate for each sample was selected for further work (n=90). Microfluidic qPCR was conducted with the 90 samples and assays for 16 different genes, 14 of which worked. See Thesis in publications section for more details. First dataset is the semi-processed data output from Fluidigm program (it does not allow the export of un-processed data). Consult Fluidigm Real-Time PCR Analysis User Guide (PN 68000088 J1) for more information on columns A-N (ID, Type, relative Conc, Value, Calibrated rConc, Quality, Threshold, In Range, Out Range, Peak Ratio). Assay = gene assayed, see Thesis in publication for more details. Name = sample name and individual extraction replicate; A,B,or C. Plate = individual Fluidigm chip; three were run, 90, 91 and 92. Time refers to sample set, see Question 2. Treatment = nominal spiking concentration of mesocosm. Dilution factor = dilution factor of sample prior to submission for microfluidic qPCR. Copies/ ul = gene copy number of DNA sample. Initial volume = extraction volume. G of soil = weight of soil extracted. Comb_cond is purely for ease of processing with factor qPCR. Factor qPCR corrected copies/g = output once interpolate differences were corrected with factor qPCR. Processed gene copy number data (copies/g) is provided in second spreadsheet in 'Biological'. 'Environmental' tab provides additional data on samples, including TPH data and vegetation observations at one time point (expressed as percentage of coverage). Contact Sarah Houlahan for more information on chemical data. Dataset Macquarie Island Southern Ocean Research Data Australia (Australian National Data Service - ANDS) Southern Ocean ENVELOPE(158.9391,158.9393,-54.4990,-54.4991) |