Difference between revisions of "DNA Melting Report Requirements"

• Follow the lab report general guidelines.
• Provide a thorough and accurate discussion of error sources and measurement uncertainty. An outstanding error discussion is an essential element of a top-notch report.
• One member of your group should submit a single PDF file to Stellar in advance of the deadline. The filename should consist of the last names of all group members, CamelCased, in alphabetical order, with a .pdf extension. Example: CrickFranklinWatson.pdf.

Part 2 report outline

1. Abstract:
   • In one paragraph of less than six sentences, summarize the investigation you undertook and key results.
2. Raw data:
   • Plot all of your raw data, fluorescence vs. block temperature, on the smallest number of axes that clearly convey the dataset. Include only datasets generated by your own group.
   • On similary-grouped sets of axes, plot ΔdsDNA fraction/Δtemperature versus temperature (example plot). See this section for details. Your plot should not look like this.
3. Model parameters:
   • Develop a model for the melting experiment and use nonlinear regression to determine best-fit parameters.
   • Explain the model parameters using bullet points or in a table.
   • Include a table of the best-fit model parameters and confidence intervals for each experimental run.
   • Use the smallest possible number of plots to show $ V_{f,measured} $ and $ V_{f,model} $ plotted versus $ \theta_{block} $.
   • Plot one of the following for at least one experimental run:
     • residuals versus time, temperature, and fluorescence, (example plot) or
     • use best-fit parameters and the inverse of your model function to transform the fluorescence voltage into dsDNA fraction versus sample temperature (example plot). Plot $ \text{DnaFraction}_{inverse-model} $ on the same set of axes with DnaFraction model data using the best-fit values of ΔH and ΔS. Also include a simulated dsDNA fraction vs. temperature curve obtained from DINAmelt or another melting curve simulator.
   • Comment on strengths and shortcomings of the model.
     • Discuss the validity of underlying assumptions.
     • Discuss the residuals (or transformed data) plot and parameter confidence intervals.
4. Unknown sample determination:
   • Plot results for your unknown sample, including those from your other samples for comparison.
   • Identify your unknown sample and state your level of confidence in the answer.
     • Confidence is quantitative.
5. Results and discussion:
   • Include a summary table of estimated thermodynamic parameters, ΔH, ΔS, and T_m. Use multiple methods to find T_m.
   • Compare your data to results from other groups or instructor data.
   • Discuss significant error sources.
     • Indicate whether each source likely caused a systematic or random distortion in the data.
     • Consider the entire system: the oligos, dye, the experimental method, and analysis methodology, and any other relevant factors.
     • Present error sources in a table, if you like.
6. Analysis:
   • Use bullet points to explain your data analysis methodology.
7. Instrument documentation:
   • Document the electronic and optical systems.
     • Include component values, gain values, cutoff frequencies, lens focal lengths, and relevant distances.
     • Feel free to reference schematics in the lab manual instead of copying them into your report. Use the reference designators (such as R7, C2) to refer to components in the schematics.
     • It is not necessary to document construction details.
   • Why not include a nice snapshot or two of the instrument?
   • Include your signal to noise results.
   • Give a bullet point summary of problems you encountered in the lab during part 2 and changes that you made to your instrument and methodology to address those issues.

Lab manual sections

• Lab Manual:Measuring DNA Melting Curves
• DNA Melting: Simulating DNA Melting - Basics
• DNA Melting Part 1: Measuring Temperature and Fluorescence
• DNA Melting Part 2: Lock-in Amplifier and Temperature Control
• DNA Melting Report Requirements