Microfluidic quantitative PCR data for in-situ Macquarie Island Mesocosm assessing the toxicity of residual hydrocarbons.

Brief 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.