Lenaolufson Week 11

Week 11 Notes From Class 11/10/15

(taken from Mahrad's notes page) DOCUMENT ALL STEPS TAKEN, MANIPULATIONS OF FILES AND ALL.

1. Experimental design-what is the treatment and what is the control

• Biological vs technical replicants- for vibrio control was the untreated strain, technical replicates = splitting a sample, different from biological replicates. Biological replicates are derived from the original strain. *note how many replicates of each. # of chips(microarrays) (for vibrio it was 9, total number of samples)
  • Dye swaps, cy3 green dye and cy5 red. note how many swaps. Swaps done to avoid dye playing an effect in replication.
    • Draw a diagram to help of how chips were obtained.

2. Sample + data relationship. In raw data there should be one file to each chip. Match file name to sample. raw.zip on arrayexpress has one file for each chip. Sdrf.txt open in excel to show whats in the samples-should tell you all of the samples, their matches, and dye swaps.

3. Compiled raw data file. Include columns for: ID, Sample log2FC, sample log2FC. Compiling raw data files into one spreadsheet to prepare for statistical analysis.

4. Normalization + statistical analysis. Customized for each dataset due to different treatments. Either t-test or one way anova. Also due sanity check, which will be a result in the paper. Compare it to what was written in the paper, corresponding to specific genes. Comparing log-fold changes of specific genes between our data and the paper's.

5. GenMAPP + mappfinder. Run data through database created by groupmates.

6. Deliverables-describing methods, production of tables including the sanity check, etc.

• In discussion compare what we found vs to what they found.

Preparation for Journal Club on Your Species

Your team will split into two halves for journal club presentations that will take place in class on Tuesday, November 17 and Tuesday, November 24. The Coder and Quality Assurance person will present the genome paper for your species and the GenMAPP Users will present the microarray paper for your species. You will decide within your team who will present on which day. Please edit the schedule on the Main Page to show who is presenting on which day.

In preparation for your journal club presentation, you will each individually complete the following assignment on your individual journal page.

1. Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries. Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. Each definition must have it's own URL citation.

• Murine: Pertaining to or affecting mice or rats.
  • http://medical-dictionary.thefreedictionary.com/murine
• Oligomerization: Formation of oligomers from larger or smaller molecules.
  • http://medical-dictionary.thefreedictionary.com/oligomerization
• Isogenic: Relating to identically identical individuals.
  • http://medical-dictionary.thefreedictionary.com/isogenic
• Ligation: The act of binding or annealing.
  • http://medical-dictionary.thefreedictionary.com/ligation
• Electroporated: A technique in which a brief electric shock is applies to cells; momentary holes open briefly in the plasma membrane, allowing the entry of macromolecules (for example, a way of introducing new DNA into a cell).
  • http://medical-dictionary.thefreedictionary.com/electroporated
• Chemiluminescent: luminescence produced by direct transformation of chemical energy into light energy.
  • http://medical-dictionary.thefreedictionary.com/chemiluminescent
• Endogenous: Produced within or caused by factors within the organism.
  • http://medical-dictionary.thefreedictionary.com/endogenous
• Intranasally: Within the nasal cavity.
  • http://medical-dictionary.thefreedictionary.com/intranasally
• Putative: Considered to exist or have existed.
  • http://www.thefreedictionary.com/putative
• Euthanized: To kill(a person or animal) painlessly, especially to relieve suffering from an incurable illness.
  • http://www.thefreedictionary.com/euthanized

1. Write an outline of the article. The length should be a minimum of the equivalent of 2 pages of standard 8 1/2 by 11 inch paper (you can use the "Print Preview" option in your browser to see the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article.
   • What is the importance or significance of this work (i.e., your species)?
   • What were the methods used in the study?
   • Briefly state the result shown in each of the figures and tables.
   • How do the results of this study compare to the results of previous studies (See Discussion).
   • For the microarray paper (GenMAPP Users only), include the following:
     1. Describe the experimental design of the microarray data, including treatments, number of replicates (biological and/or technical), dye swaps.
     2. Determine the sample and data relationships, i.e., which files in the data correspond to which samples in the experimental design.
     3. Construct a flow chart that illustrates the above.