Rigor and Reproducibility
Eight steps to Rigorous and Reproducible Experiments in Biomolecular Research at UNC:
- If using a core facility, consult with the core staff in the planning stage. Consult with a statistician if you need help developing a Power Analysis to assure that your results will be adequately powered.
- Design your experiment with sufficient controls (rigor) and replicates (reproducibility).
- Assure that ALL of your reagents (antibodies, cell lines, mice) are fully validated (see below).
- Have a clear and detailed protocol (SOP) and data analysis plan. Assure that the protocol is strictly followed or that any deviation is well documented.
- Assure that the staff or students performing the experiment are well trained and understand each step and the importance of performing them precisely.
- Use only well-maintained instrumentation, preferably maintained and operated in a core facility with expert staff (see #1 above).
- Document all steps, reagents, equipment and data analysis methods used in the experiment. Assure that the both the documentation and the data itself are properly stored in a safe data management repository.
- Acknowledge the Cancer Center Support Grant (P30 CA016086) (if applicable), other grants that support the core, the core (by name), and core staff in publications.
Guide to Rigor and Reproducibility for the UNC Microbiome Core
- Consult with the core staff in the planning stage.
- To improve the quality and reproducibility of microbiome analyses, the microbiome core facility utilizes microbial reference materials. The ZymoBIOMICS Microbial Community Standard is the first commercially available standard for metagenome studies. The microbial standard is a well-defined, accurately characterized mock community consisting of Gram-negative and Gram-positive bacteria and yeast with varying sizes and cell wall composition. The wide range of organisms with different properties enables characterization, optimization, and validation of lysis methods such as bead beating. It can be used as a defined input to assess the performance of entire metagenomic workflows, therefore enabling workflows to be optimized and validated. A mock microbial DNA community standard allows the core facility to focus the optimization after the step of DNA extraction.
- Established resources and vendors are used for all microbiome analysis. If possible, all samples belonging to a project are processed within the same batch (to avoid batch bias) and with the same lot of reagents (to avoid lot-to-lot variations). Protocols used in the Core are compliant with the guidance provided by the MicroBiome Quality Control (MBQC) project and the National Institute of Standards and Technology (NIST).
- Standard Operating Procedures (SOPs) and protocols are available at the Microbiome Core upon request.
- Preventative maintenance of instruments in the Microbiome Core is conducted on an annual or semi-annual schedule.
- Detailed descriptions of experimental procedures including sample storage and processing are documented electronically and in notebooks. Instruments and settings used for all experiments are detailed with the associated experiment electronically and in laboratory notebooks.
- Please acknowledge the UNC Microbiome Core, Cancer Center Support Grant (P30 CA016086) and Center for Gastrointestinal Biology and Disease in your publications (P30 DK34987).