Difference between revisions of "DNA Melting Report Requirements"
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##Single set of axes with plots of ΔdsDNA concentration/Δtemperature vs temperature for same. | ##Single set of axes with plots of ΔdsDNA concentration/Δtemperature vs temperature for same. | ||
##Similar figure, single axes, showing results for unknown sample, possibly including other samples run for comparison. | ##Similar figure, single axes, showing results for unknown sample, possibly including other samples run for comparison. | ||
| − | #;Model Parameter Determination: | + | #;Model Parameter Determination: For each sample type, show a comparison of your data to a modeled sigmoidal curve from the thermodynamic model, and compare each to a simulated result obtained from DINAmelt or another melting curve simulator. |
| − | ##These plots should be in the "ideal" format. For each sample type: Fit a model to your melting curve data. Correct the data using the parameters obtained from your fit. Average the corrected curves for all successful runs of that sample type. Finally, compare each of those corrected, averaged curves to the ideal curve for that sample type. (Ideal curves are obtained using your fitted ΔS and ΔH in the basic thermodynamic model.) | + | ##These plots should be in the "ideal" format. For each sample type: |
| − | ##Also include an example or two of plots in the "as-observed" format, showing your model | + | ###Fit a model to your melting curve data. |
| + | ###Correct the data using the parameters obtained from your fit. | ||
| + | ###Average the corrected curves for all successful runs of that sample type. | ||
| + | ###Finally, compare each of those corrected, averaged curves to the ideal curve for that sample type. (Ideal curves are obtained using your fitted ΔS and ΔH in the basic thermodynamic model.) | ||
| + | ##Also include an example or two of plots in the "as-observed" format, showing that your model fit well to the as-observed data. For these examples, also include a plot of a modeled response using your initial guesses. | ||
#;Unknown determination: Finally, include averaged, corrected data and a modeled response for your unknown sample either on the above dsDNA and ΔdsDNA plots, or in separate plots. | #;Unknown determination: Finally, include averaged, corrected data and a modeled response for your unknown sample either on the above dsDNA and ΔdsDNA plots, or in separate plots. | ||
#;Table of estimated thermodynamic parameters for each sample. Include estimated ΔH, ΔS, and T<sub>m</sub> values (by multiple methods) | #;Table of estimated thermodynamic parameters for each sample. Include estimated ΔH, ΔS, and T<sub>m</sub> values (by multiple methods) | ||
Revision as of 23:20, 7 November 2012
Report outline
Use the following format for your report:
- Report submittal format
- Size of your lab manual file submitted MUST be less than 20 MB
- Post only pdf, with code included in the pdf at the end, not separately
- Include last name of each group member in the filename of the pdf you post. I would rather spend time carefully grading your report than renaming your files because every other group named theirs "DNA Report Part 2" or the like.
- Results
- Samples run
- List all of the samples you characterized (length/match/ionic strength)
- Data plots
- All plots should be complete with title, axis labels, and legend. Plot both your experimental data and the best fit curves from the DNA melting mode. Plots in this section should include only data that was created by your group's own hands in the lab. Analysis of other people's datasets belongs in a different section (see below).
- Single set of axes with plots of dsDNA concentration versus temperature for ALL raw data from all "known" samples that you ran.
- Single set of axes with plots of ΔdsDNA concentration/Δtemperature vs temperature for same.
- Similar figure, single axes, showing results for unknown sample, possibly including other samples run for comparison.
- Model Parameter Determination
- For each sample type, show a comparison of your data to a modeled sigmoidal curve from the thermodynamic model, and compare each to a simulated result obtained from DINAmelt or another melting curve simulator.
- These plots should be in the "ideal" format. For each sample type:
- Fit a model to your melting curve data.
- Correct the data using the parameters obtained from your fit.
- Average the corrected curves for all successful runs of that sample type.
- Finally, compare each of those corrected, averaged curves to the ideal curve for that sample type. (Ideal curves are obtained using your fitted ΔS and ΔH in the basic thermodynamic model.)
- Also include an example or two of plots in the "as-observed" format, showing that your model fit well to the as-observed data. For these examples, also include a plot of a modeled response using your initial guesses.
- Unknown determination
- Finally, include averaged, corrected data and a modeled response for your unknown sample either on the above dsDNA and ΔdsDNA plots, or in separate plots.
- Table of estimated thermodynamic parameters for each sample. Include estimated ΔH, ΔS, and Tm values (by multiple methods)
- Comparative data analysis and plots
- Plots of any data you analyzed that came from other groups
- Data analysis overview
- Informative Bullet point summary of your data analysis methodology. Teach us what you did.
- Discussion of results
- Bullet point discussion of results. Compare your results to theoretical models and/or other group's datasets. Be concise, but express yourself clearly.
- Sources of error:Detailed discussion of error sources. Indicate whether each source causes a systematic or random distortion in the data. (The uncertainty from a random error decreases with additional experimental runs; systematic error does not.) Consider all possible sources of error including all aspects of your instrument, the oligo design, the dye used, the experimental methodology, and the analysis methodology.
- Instrument documentation
- Block diagram and schematics
- Include component values, relevant distances, and possibly a photograph or two. It is not necessary to document construction details, but do show your work in determining your component values, distances, etc.
- Signal to noise results
- Design evolution
- 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
