Difference between revisions of "The Class Whoopers"

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# Were replicate experiments of the "treatment" and "control" conditions conducted?  Were these biological or technical replicates?  How many of each?
 
# Were replicate experiments of the "treatment" and "control" conditions conducted?  Were these biological or technical replicates?  How many of each?
 
* Link to microarray data: https://www.ebi.ac.uk/arrayexpress/experiments/E-TABM-28/
 
* Link to microarray data: https://www.ebi.ac.uk/arrayexpress/experiments/E-TABM-28/
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===Mahrad Saeedi===
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Genome Sequencing Paper:
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King, Audrey J et al. “Comparative Genomic Profiling of Dutch Clinical Bordetella Pertussis isolates Using DNA Microarrays: Identification of Genes Absent from Epidemic Strains.” BMC Genomics 9 (2008): 311. PMC. Web. 10 Nov. 2015.
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* PubMed Abstract:  http://www.biomedcentral.com/1471-2164/9/311#abs
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* PubMed Central: <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2481270/>
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* Publisher Full Text (HTML):  http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2481270/
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* Publisher Full Text (PDF): <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2481270/pdf/1471-2164-9-311.pdf>
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* Copyright:  © 2008 King et al; licensee BioMed Central Ltd.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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* Publisher: BMC Genomics
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* Availability: online access
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* Did LMU pay a fee for this article: no
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Microarray Paper:
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Nakamura, Mari M. et al. “Growth Phase- and Nutrient Limitation-Associated Transcript Abundance Regulation in Bordetella Pertussis  .” Infection and Immunity 74.10 (2006): 5537–5548. PMC. Web. 10 Nov. 2015.
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* PubMed Abstract:  <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1594893/?report=reader#__abstractid499869title>
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* PubMed Central: <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1594893/>
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* Publisher Full Text (HTML): <http://iai.asm.org/content/74/10/5537.full>
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* Publisher Full Text (PDF):  <http://iai.asm.org/content/74/10/5537.full.pdf+html>
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* Copyright: © 2006, American Society for Microbiology
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* Publisher: Infection and Immunity
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* Availability: online access
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* Did LMU pay a fee for this article: no
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== Deliverables ==
 
== Deliverables ==

Revision as of 04:22, 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)

Brandon's Citations

Genome Sequencing Paper:

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

Microarray Papers:

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

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 2014;9(12):e115243. doi: 10.1371/journal.pone.0115243

Lena's Citations

Genome Sequencing Paper:

Microarray Paper:

Microarray Paper:

Nicole Anguiano

  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?


  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?

Mahrad Saeedi

Genome Sequencing Paper:

King, Audrey J et al. “Comparative Genomic Profiling of Dutch Clinical Bordetella Pertussis isolates Using DNA Microarrays: Identification of Genes Absent from Epidemic Strains.” BMC Genomics 9 (2008): 311. PMC. Web. 10 Nov. 2015.

Microarray Paper:

Nakamura, Mari M. et al. “Growth Phase- and Nutrient Limitation-Associated Transcript Abundance Regulation in Bordetella Pertussis .” Infection and Immunity 74.10 (2006): 5537–5548. PMC. Web. 10 Nov. 2015.


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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