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. Intro and Purpose:
   • Provide a succinct introduction to the project including the purpose of the experiment and relevant background material and/or links to such information.
   • Note the ways in which this part of the lab differs from Part 1.
   • Keep the length to one short paragraph, no more than 1/3 of a page.
3. Apparatus:
   • Document the critical components and operational parameters of your instrument that would be necessary for another to replicate your work. Focus on the electronic and optical subsystems.
     • 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?
4. Procedure:
   • Document the procedure used to gather your data. As above, include only information beyond that of the lab manual, but provide information necessary to reproduce your results.
5. 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 a similar number of axes, with perhaps the same grouping of sample types, plot ΔdsDNA fraction/Δtemperature versus temperature (example plot). See this section for details. Your plot should not look like this.
   • ... something about raw signal and band-passed PSDs screen-captured from GUIs ...
   • Include your signal to noise results.
6. Analysis:
   • 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.
   • Use bullet points to explain your data analysis methodology. In particular, explain the use of your model toward determination of your primary outcome: a measure of the oligo melting temperature.
   • To demonstrate that your model visibly fits the measured data, provide one or two representative examples of $ V_{f,measured} $ and $ V_{f,model} $ plotted versus $ \theta_{block} $.
   • For the same data sets and fit, plot residuals versus time, temperature, and fluorescence, (example plot) and comment on the results.
7. Results:
   • Provide a table of the best-fit model parameters and confidence intervals for each experimental run.
     • Highlight the estimated thermodynamic parameters, ΔH, ΔS, and T_m. Use multiple methods to find T_m.
     • Discuss the confidence with which the model parameters have been determined. Confidence is quantitative.
   • For all experimental trials, use the inverse of your model function $ \text{DnaFraction}_{inverse-model} $, the best-fit parameters and the observed fluorescence to plot dsDNA fraction versus sample temperature (example plot). On the same set of axes plot 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.
     • Present these plots on the smallest number of axes possible that clearly conveys your results. Hint: Avoid overlapping plots unless those plots result from the same sample type.
   • 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.
8. Discussion:
   • 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.
   • 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.
   • 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.
     • Present error sources in a table, if you like.
9. Conclusion:
   • Restate the highlights of the report and present final, summary comments on the experiment.
   • Make note of any surprising results.
   • Restate your determination of the unknown sample type and the confidence of that determination.
   • Discuss changes that improved the instrument.
   • Discuss changes that would improved your analysis toward a more confident sample determination, if that is necessary.
   • Comment on any other recommended changes for future DNA Melting Lab modules.

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