Difference between revisions of "DNA Melting Report Requirements"
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#* Develop a model for the melting experiment and use nonlinear regression to determine best-fit parameters. | #* Develop a model for the melting experiment and use nonlinear regression to determine best-fit parameters. | ||
#* Explain the model parameters using bullet points. | #* Explain the model parameters using bullet points. | ||
− | #* Use the smallest possible number of plots to compare the model with best-fit parameters to your data and a simulated result obtained from DINAmelt or another melting curve simulator. | + | #* 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. |
+ | #* Either plot 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. | ||
# Unknown sample determination: | # Unknown sample determination: | ||
#* Plot results for unknown sample, including other samples for comparison. | #* Plot results for unknown sample, including other samples for comparison. | ||
#* Identify your unknown sample and state your level of confidence in the answer. | #* 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. | #*Use the smallest possible number of plots to compare the unknown sample to the corresponding known sample. | ||
− | # | + | # Results and discussion |
+ | #* Include a table of estimated thermodynamic parameters, ΔH, ΔS, and T<sub>m</sub>. Use multiple methods to find T<sub>m</sub>. | ||
#* Compare your data to results from other groups or instructor data. | #* Compare your data to results from other groups or instructor data. | ||
# Analysis | # Analysis | ||
#* Use bullet points to explain your data analysis methodology. | #* Use bullet points to explain your data analysis methodology. | ||
− | |||
− | |||
# Error sources | # Error sources | ||
#* Discuss important error sources. | #* Discuss important error sources. |
Revision as of 02:56, 16 November 2012
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
- 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. 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.
- 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.
- Either plot 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.
- 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.
- 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.
- Analysis
- Use bullet points to explain your data analysis methodology.
- 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.
- 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