Difference between revisions of "The Class Whoopers"

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(→‎Microarray Papers)
(→‎Genome Sequencing Paper: corrected genome paper)
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* [[Week 10]] Creation of page and combined annotated bibliography (midnight 11/10)
 
* [[Week 10]] Creation of page and combined annotated bibliography (midnight 11/10)
 
=== Genome Sequencing Paper ===
 
=== Genome Sequencing Paper ===
 +
 +
Neither of these papers is the ''first'' to report the genome sequence of ''B. pertussis.''  The paper that you will want to use is [http://www.nature.com/ng/journal/v35/n1/full/ng1227.html this one].  I found it by looking at the introduction and references of the Zhang et. al (2011) paper.  For your Week 11 assignment, please remove your annotated bibliography entries for the two papers below and create one for this new paper by Parkhill et al. (2003).  You will use the Parkhill paper for your project.  ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 09:54, 10 November 2015 (PST)''
  
 
*Zhang, S., Xu, Y., Zhou, Z., Wang, S., Yang, R., Wang, J., & Wang, L. (2011). Complete Genome Sequence of Bordetella Pertussis CS, a Chinese Pertussis Vaccine Strain. Journal of Bacteriology, 193(15), 4017-4018. doi: 10.1128/JB.05184-11
 
*Zhang, S., Xu, Y., Zhou, Z., Wang, S., Yang, R., Wang, J., & Wang, L. (2011). Complete Genome Sequence of Bordetella Pertussis CS, a Chinese Pertussis Vaccine Strain. Journal of Bacteriology, 193(15), 4017-4018. doi: 10.1128/JB.05184-11

Revision as of 17:54, 10 November 2015

The Class Whoopers Crew Page

The_Class_Whoopers

  • Species: Bordetella pertussis

Crew Members

Team Goals for the Week of 11/3

  • For all:
    • Make an annotated bibliography of 1-2 articles (preferably 2) on Bordetella pertussis following the instructions here, and post them on your individual journal page!
    • Once everyone has done their bibliographies, we'll discuss a ranking of which we think are the best ones and list them below in ranked order. Try to find different articles from everyone else so we have the maximum number of options.

Meetings!

  • Monday, November 9, 8pm, Seaver 120

Annotated Bibliography

  • Week 10 Creation of page and combined annotated bibliography (midnight 11/10)

Genome Sequencing Paper

Neither of these papers is the first to report the genome sequence of B. pertussis. The paper that you will want to use is this one. I found it by looking at the introduction and references of the Zhang et. al (2011) paper. For your Week 11 assignment, please remove your annotated bibliography entries for the two papers below and create one for this new paper by Parkhill et al. (2003). You will use the Parkhill paper for your project. — Kdahlquist (talk) 09:54, 10 November 2015 (PST)

(Note: The below paper is very similar to the genome sequencing paper listed above but more recent. We were unsure how to designate which of the two would be a better paper. If possible, feedback regarding which to choose would be appreciated. Otherwise, we would like to use the above genome sequencing paper.)

Microarray Papers

1

Hoo, R., Lam, J.H., Huot, L., Pant, A., Li, R., Hot, D., & Alonso, S. (2014). Evidence for a Role of the Polysaccharide Capsule Transport Proteins in Pertussis Pathogenesis. PLoS ONE, 9(12):e115243. doi: 10.1371/journal.pone.0115243

2
3

King, A. J., van der Lee, S., Mohangoo, A., van Gent, M., van der Ark, A., & van de Waterbeemd, B. (2013). Genome-Wide Gene Expression Analysis of Bordetella pertussis Isolates Associated with a Resurgence in Pertussis: Elucidation of Factors Involved in the Increased Fitness of Epidemic Strains. PLoS ONE, 8(6): e66150. doi: 10.1371/journal.pone.0066150

4 (note, all of the papers from this point on involve additional species other than Bordetella pertussis)
5
  1. What experiment was performed? What was the "treatment" and what was the "control" in the experiment?
  2. Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each?
6
  1. What experiment was performed? What was the "treatment" and what was the "control" in the experiment?
  2. Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each?
7
8

Deliverables

  • GenMAPP Gene Database for assigned species (.gdb)
  • ReadMe file to accompany the Gene Database (.pdf)
  • Sample ReadMe in Word format: ReadMe_Vc-Std_External_20131122.zip
  • Include Gene Database Schema diagram in ReadMe
  • Sample schema in Adobe Illustrator format: Vibrio_schema_20101022.zip
  • Gene Database Testing Report for final submitted Gene Database (print from wiki to .pdf file)
  • Processed and analyzed DNA microarray dataset (.xls)
  • GenMAPP Expression Dataset file (.gex)
  • Filtered MAPPFinder Results (.xls)
  • Sample MAPP file of a relevant biological pathway for your species (.mapp)
  • Group Report describing the creation of the Gene Database and the biological analysis of the data (.doc or .pdf)
  • PowerPoint presentation (.ppt, given on Tuesday, December 15)


Links

GenMAPP Analysis of Bordetella pertussis Microarray Data

Gene Database Project Links
Overview Deliverables Reference Format Guilds Project Manager GenMAPP User Quality Assurance Coder
Teams Heavy Metal HaterZ The Class Whoopers GÉNialOMICS Oregon Trail Survivors

Journal Entries

Class Whoopers Individual Journal Entries
Brandon Klein Week 11 Week 12 Week 14 Week 15
Lena Olufson Week 11 Week 12 Week 14 Week 15
Mahrad Saeedi Week 11 Week 12 Week 14 Week 15
Team Entries Week 11 Week 12 Week 14 Week 15

Group Members

Team Weekly Assignments

  • Week 10 Creation of page and combined annotated bibliography (midnight 11/10)
  • Week 11 (midnight 11/17)
  • Week 12 (midnight 11/24)
  • Week 14 (midnight 12/8)
  • Week 15 (midnight 12/15)
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