Difference between revisions of "20.109(S07): Microarray data analysis"

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DONE!
 
DONE!
 
==For next time==
 
==For next time==
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Your first draft of your Mod 3 lab report is due next time. Remind yourself of the class expectations for [http://openwetware.org/wiki/20.109%28S07%29%3AGuidelines_for_writing_a_lab_report your report]. Some extra information to guide you when you prepare your Mod3 lab report is included here.
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Your first draft of your Mod 3 lab report is due next time. Remind yourself of the class expectations for [http://openwetware.org/wiki/20.109%28S07%29%3AGuidelines_for_writing_a_lab_report your report]. Some extra information to guide you when you prepare your Mod3 lab report is included [[20.109(S07): Expression engineering report| here]]
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===Abstract===
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*Please keep the number of words under 250.
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*Do not include references in the abstract.
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*Try drafting this section after you’ve written the rest of the report.
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*If you’re truly stuck, start by modifying one crystallizing sentence from each of the sections of your report.
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*Please do not plagiarize (accidentally or other) the class wiki. This applies to your entire report.
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===Introduction===
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The homework you wrote after the first day of this new module will serve at the heart of your introduction. You should add (at least) one final paragraph to narrow the information “funnel,” ending your introduction with a clear description of the problem you’re studying and the method you are using. If you would like to preview for the reader your key results and conclusions in the last sentence of your introduction, you may.
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===Materials and Methods===
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If you used any kits for any of the manipulations, it is sufficient to cite the manufacturer’s directions, e.g. “yeast were transformed according to the Q-biogene transformation kit protocol.”
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Subdivide this section into the following
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#Yeast strains and plasmids
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#*list genotypes and plasmid names when known
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#PCR
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#*include primer design info here
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#*include primer sequences, for knockout and for candidate verification
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#*include PCR cycling conditions
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#Yeast transformation
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#* include how you selected for transformants
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#* include what you did to verify that URA3 was integrated where you thought.
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#Yeast Microarray
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#*mention kits as relevant, including any deviation from published protocol if any
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#*mention how many yeast and how much RNA was used
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#*describe array analytical methods in results section rather in Materials and Methods
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===Results===
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====figures====
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You should include but are not limited to the following figures and tables
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#Figure 1
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#*panel A: table describing transformation results
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#*panel B: agarose gel verifying URA3 insertion
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#Figure 2
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#*Spot test images
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#Figure 3
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#*microarray analytics
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#Figure 4
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#*microarray conclusions
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Each figure should be numbered, and should have a title and legend
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====text====
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*In paragraph form, describe each figure and the observations you made.
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*As much as possible, reserve conclusions about your data for the discussion section. Clearly an exception to this will be which of your deletion candidates was correct, as this information is critical for the next steps in the experiments.
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===Discussion===
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You should include but are not limited to
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*conclusions you can draw from your work, including any uncertainties
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*other data (published or personal communications) that support or contradict your conclusions
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*limitations of your work, e.g. what kinds of experiments/controls/samples would have been great to include
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*next experiments you would like to try to extend your findings and strengthen your conclusions
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Revision as of 19:42, 11 January 2007


20.109: Laboratory Fundamentals of Biological Engineering

Macintosh HD-Users-nkuldell-Desktop-20.109template.png

Home        People        Schedule Spring 2007        Lab Basics        OWW Basics       
Genome Engineering        Biophysical Signal Measurement        Expression Engineering        Biomaterial Engineering       

Introduction

Protocols

Here is a rough outline of the steps you can take to examine your microarray data. There are many variations on this that are acceptable and that may be more interesting or appropriate for you. You should explore the data as you see fit.

  1. open txt file in xls (tab delimited)
  2. delete top 21 rows
  3. label a new worksheet for working with your data
  4. copy columns for: GeneName, SystematicName, Description, gMeanSignal, rMeanSignal gMedianSignal, rMedianSignal, gBGMeanSignal, rBGMeanSignal, gBGMedianSignal, rBGMedianSignal
  5. format the numberical cells as numbers with no decimal place
  6. consider mean and median variations and background, to correct as you see fit. Be sure you keep track in your notebook or in the xls file of your analytical decisions.
  7. start new column with ratio of green signal/red signal.
  8. start new column called log2green/red and use data in green/red column as =LOG(cell#,base), for example =LOG(D3,2) and drag corner to apply formula to all 11K cells. Again format to whole numbers if this does not happen automatically.
  9. Select entire sheet by clicking on diamond in corner then sort by log2 (green/red).
  10. Sort cells in decending order according to log2green/red
  11. What do you see? Are the duplicates in agreement? Are there particular genes you expect to see up or down regulated in the two samples (e.g. URA3)? What happens to the SAGA-subunits? Are there particular kinds of genes (e.g. mating type genes, gal regualated genes...) that are up or down regulated by the deletion? Ask the questions you want about this data...
  12. save as XLS worksheet or workbook

DONE!

For next time

Your first draft of your Mod 3 lab report is due next time. Remind yourself of the class expectations for your report. Some extra information to guide you when you prepare your Mod3 lab report is included here

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