DNA Melting Report Requirements
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Revision as of 21:31, 18 November 2012 by Steven Wasserman (Talk | contribs)
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
- Abstract:
- In one paragraph of less than six sentences, summarize the investigation you undertook and key results.
- 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.
- 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.
- 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.
- Results and discussion
- Include a table of estimated thermodynamic parameters, ΔH, ΔS, and Tm. Use multiple methods to find Tm.
- 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.
- Analysis
- Use bullet points to explain your data analysis methodology.
- 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?
- Document the electronic and optical systems.
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