Appendix B: Minimum Details to Report for Routine Laboratory Methods

The following are the critical details required to replicate common biochemical techniques. At minimum you must include these details in your methods and captions.

  • Agarose gel electrophoresis
    • Captions: percent agarose; identity of running buffer; staining methodology; approximate mass of sample DNA loaded per lane; identity of lanes; identity of important bands in reference ladder.
    • Methods: percent agarose; composition and pH of buffer used to make and run the gel; amount of sample loaded; type of reference ladder used; manufacturer of reference ladder; voltage per cm; time; staining procedure; visualization method (i.e. trans-illumination, epi-illumination), wavelength of light.
  • Chromatography
    • Captions: method (e.g. column, thin layer); stationary phase (e.g. silica, Dowex 50WX4); composition of mobile phase; visualization procedure; identity of samples.
    • Methods: method (e.g. column, thin layer); identity (e.g. silica, Dowex 50WX4) and amount (e.g. height and diameter for column, dimensions for TLC plate) of stationary phase; composition of mobile phase; flow rate and gradients (for column); total time (for plate); visualization procedure.
  • Compositions of solutions
    • Methods: state composition solutions and buffers (e.g. 100 mM Tris buffer, pH 8.50 with 50 mM NaCl); you do not need to describe the recipes to make concentrated stocks and steps you carried-out to prepare the buffer.
  • Data plot (general)
    • Captions: if a figure has a trendline, give the equation of the trendline (with units) and the R2 value in the caption.
    • Methods: describe your methods of data analysis, important equations, and calculations used. Define non-standard units. If you analyzed and plotted your data using spreadsheet software, you must name the software package and manufacturer.
  • Enzyme kinetics data
    • Captions: identify the enzyme, substrate, buffer, and temperature. Identify what was measured and what variables were changed (if applicable). Provide the equation of the trendline (with units) and the R-squared value.
    • Methods: provide the final composition  and pH of buffer used (state manufacturer if commercial buffer); final concentrations of all components (e.g. substrate, BSA, ATP); if commecial reagents were used, state volume, stock concentration, and manufacturer for each; if assaying an enzyme solution of unknown composition, provide volume of enzyme solution added; if assaying a known enzyme solution, state either the total units of activity or mass of enzyme added; total volume of the assay; time; temperature; model and manufacturer of instrumentation used to measure (e.g. Thermo Spectronic 20, etc.); identify the parameter that was monitored over time (e.g. wavelength, mass ion); identity of the blank used as the zero reference; describe your methods of data analysis; provide important equations; name the software (package and manufacturer) and explain what features were used; define your activity units.
  • Enzymatic reactions for substrate conversion with commercial kits
    • Methods: provide the volume and identity of buffer used (state manufacturer), volumes of additives added (e.g. BSA, ATP; state concentration and manufacturer), volume of sample added (state concentration), total volume, time, temperature.
  • Polyacrylamide gel electrophoresis (PAGE)
    • Captions: percent of acrylamide in gel; staining methodology; identity of lanes; identity of important bands in reference ladder.
    • Methods: percent of acrylamide in gel; composition of the running buffer; approximate amount of sample loaded; type of ladder used including manufacturer; voltage; time; staining procedure with sufficient detail; imaging method (i.e. trans-illumination, epi-illumination ) including wavelength of light.
  • Protein assay (colorimetric methods)
    • Captions: Plot the standard curve; identify the protein standard; identify they type of assay, state the wavelength observed, give the equation of the trendline (with units) and the R2 value in the caption.
    • Methods: The methods used for one assay must be the same for all samples, standards, and controls). First, describe these conditions and then provide the details for the different types of analytes. The state the volumes of reagents and analytes used to prepare one assay. For the reagents, provide either the composition or product information (name and manufacturer) in parentheses. Provide the experimental details: development time and temperature, model and manufacturer of instrumentation (e.g. Thermo Spectronic 20, etc.), and wavelength(s) measured. For the analytes, identify the protein standard and mass range used (alternatively give stock concentration and volume range used); provide the volume (or volume range) of sample added (if diluted, state the sample dilution factor); and identity of the blank used as the negative control. Describe your methods of data analysis (e.g. standard curve plots); explain general process for converting standard curve to a sample concentration; name the software package and manufacturer.
  • Spectrophotometric measurements
    • Model and manufacturer of spectrophotometer (e.g. Thermo Spectronic 20, etc.); wavelength(s) measured; identity of the blank used as the zero reference; dilutions made on sample (if applicable).
  • Titration
    • Captions: Present a scatter-plot with volume of titrant on the x-axis and the measured parameter (e.g. pH) on the y-axis; state the concentration and identity of the titrant; explain any lines that correspond to the approximately linear regions before, through, and after the break; state the volume(s) of the equivalence point(s); identify critical y-axis values derived from the plot (e.g. the pKa). 
    • Methods:  Describe how the titration was conducted (mention stirring, use of a burret, etc.); describe what parameter was measured (e.g. pH, voltage, or describe the endpoint); state the concentration of the titrant.