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.
• 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. 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).

   1. Single set of axes with plots of dsDNA concentration versus temperature for ALL raw data from all "known" samples that you ran.
   2. Single set of axes with plots of ΔdsDNA concentration/Δtemperature vs temperature for same.
   3. 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.

   1. These plots should be in the "ideal" format. For each sample type:
      1. Fit a model to your as-observed melting curve data by applying corrections to the ideal curve output by DnaFraction.m. For temperature input to DnaFraction.m, use a predicted sample temperature based on the measured heating block temperature.
      2. Now use the parameters found in that fit and the inverse of your corrections to scale the data to make it look like the ideal model, plotted vs the predicted sample temperature.
      3. Average the scaled curves for all successful runs of that sample type.
      4. Compare each of those averaged, scaled curves to the ideal sigmoidal curve for that sample type obtained using the ΔS and ΔH you obtained by fitting your model.
      5. In the same figure, show the melting curve predicted by simulation with DINAMelt of equivalent.
   2. Also, in a separate figure include an example or two of plots in the "as-observed" format, showing that your model fit well to the as-observed data, and showing your initial guess(es).

   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.

   Include a table of estimated thermodynamic parameters for each sample. Include estimated ΔH, ΔS, and T_m values (by multiple methods)

   Show comparative data analysis and plots

   Plots of any data you analyzed that came from other groups.

   Give a data analysis overview using an informative Bullet point summary of your data analysis methodology. Teach us what you did.

   Discuss your results

   Compare your results to theoretical models and/or other group's datasets. Be concise, but express yourself clearly.

2. Sources of error: Provide a 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.
3. 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

   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