Best practices for laboratory quality control
We recommend following the PCR Applications Manual by Roche for preventing contamination in the PCR laboratory and cultivating habits that prevent cross-contamination. Use physically separate areas and designated pipettes are used for sample preparation, preparation of reagents, DNA extraction, RNA extraction, PCR amplification, and post-PCR analysis. Use filtered tips and controls for all reactions. Make sure pipettes and equipment is calibrated annually.
Reagents and standards:
Chemicals are barcoded and registered with NU Environmental Health and Safety. Reagents made in-house are should be barcoded, aliquoted and barcoded again for individual projects, and the barcodes are tracked in lab notebooks. Important reagents (adapters and oligos) are handled by a designated person, who will make individual aliquots that are also barcoded and tracked in lab notebooks. For normal protocols, a set of “gold standards” should be designated, which are used to benchmark new chemicals/reagents and troubleshoot when necessary. Always use ultrapure water for reagent and sample dilution. To reduce cross-contamination, every person working in the lab is responsible for maintaining a clean working environment and their own set of aliquots for projects. Use cleaning agents that are suitable for and dedicated to decontaminating PCR lab surfaces and instruments, and UV irradiation in a specialized hood.
Version control and data analysis:
Version control for all lab data analysis projects should be maintained with Git or on Github. Follow recommended organization schemes for large data projects from Data Carpentry and Bioinformatics Data Skills (Buffalo 2015, O’Reilly Media). To maintain that intermediate outputs and parameter choices are well documented, lab personnel should be required to keep electronic notebooks and logs that document what code was run and what the output was.