Difference between revisions of "DNA Melting Report Requirements"

Format

• One group member must submit a single PDF file no larger than 20 MB to Stellar before the deadline.
• The name of the submitted file must consist of the last name of each group member separated by underscores: <LastName1>_<LastName2>_<LastName2>.pdf
• Include computer code in an appendix at the end of the file. Do not submit code separately.
• Present data properly. Follow the 20.309:Lab Report Guidelines. Include a descriptive title, axis labels, and legend on all plots.
• Begin the report with a cover page that lists the full names of group members, your assigned DNA sample number, the type of investigation (length/ionic strength/complementarity), and a haiku about DNA melting curves.

Failure to follow the format guidelines will result in ridiculously large grade penalties

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 group's 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. Filter high-noise outliers in the derivative where appropriate.
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.
   • 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} $
   • Plot one of the following for at least one experimental run:
     • residuals versus time, temperature, and fluorescence, (example plot: [1]) 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: [2]). Plot this 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 versus 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 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.
     • 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 major changes that you made to your instrument design between the end of Part 1 and the end of Part 2 to address problems in the lab.
     • What were those problems and how well did each change address it?

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 Report Requirements for Part 1
• DNA Melting: Simulating DNA Melting - Intermediate Topics
• DNA Melting Part 2: Lock-in Amplifier and Temperature Control
• DNA Melting Report Requirements for Part 2