DNA was extracted from both initial mixtures (0-h incubation) and end point co-cultures (72-h incubation) using the DNeasy Power Biofilm extraction kit (DNeasy PowerBiofilm, Qiagen, Mississauga, ON) as described previously [5 (link)], except that both planktonic (i.e. supernatant of each well) and biofilm fractions (scraped with a pipette tip from the bottom of the 96-well plates) were combined for DNA extraction. Negative controls containing kit reagents only were included for all batches of DNA extractions to identify any systemic contamination of reagents and control for cross-contamination, and these controls were carried through the PCR, library preparation and sequencing process.
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Comprehensive DNA Extraction from Biofilm and Planktonic Fractions
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Biofilm
Co cultures
Library
Planktonic
Corresponding Organization :
Other organizations : University of Saskatchewan
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Variable analysis
independent variables
- Incubation time (0-h and 72-h)
- DNA extracted from initial mixtures (0-h incubation) and end point co-cultures (72-h incubation)
- Experimental method (DNeasy Power Biofilm extraction kit)
- Combining of planktonic and biofilm fractions for DNA extraction
- Negative controls containing kit reagents only
- Negative controls containing kit reagents only
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