Difference between revisions of "DNA Melting Report Requirements"

Format

• One group member must submit a single PDF file no more 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.
• All plots must be presented properly, including a descriptive title, axis labels, and legend.
• Begin the report with a cover page the lists the full names of all 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. temperature, on the smallest number of axes that clearly convey the dataset. Include only data datasets generated by your own group.
   • On similary-grouped sets of axes, plot ΔdsDNA fraction/Δtemperature.
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 model parameters and confidence intervals for each experimental run.
   • Use the smallest possible number of fluorescence voltage vs. temperature plots to compare the model with best-fit parameters to your data and a simulated result obtained from DINAmelt or another melting curve simulator.
   • Plot one of the following:
     • residuals versus time, temperature, and fluorescence, or
     • use best-fit parameters to transform the fluorescence voltage into dsDNA fraction versus temperature for at least one experimental run.
   • Comment on strengths and shortcomings of the model.
     • Discuss validity of underlying assumptions.
     • Discuss the residuals (or transformed data) plot and parameter confidence intervals.
4. Unknown sample determination:
   • Plot results for unknown sample, including other samples for comparison.
   • Identify your unknown sample and state your level of confidence in the answer.
   • Use the smallest possible number of plots to compare the unknown sample to the corresponding known sample.
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.
6. Analysis
   • Use bullet points to explain your data analysis methodology.
7. Error sources
   • Discuss important error sources.
   • Indicate whether each source causes a systematic or random distortion in the data.
   • Consider the entire system: the oligos, dye, the experimental method, and the analysis methodology.
   • Present error sources in a table, if you like.
8. 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?
   • Signal to noise results
   • Give a bullet point summary of changes you made to your instrument design to address problems in the lab.

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