Difference between revisions of "Talk:Chlamydia trachomatis"

Revision as of 00:16, 14 November 2013

GenMAPP User Notes

Week 10 Feedback

• Thank you for submitting your team page on time.
• We are expecting roughly equal contributions from all team members; Dillon only made a few saves compared to Katrina and Hilda.
• As for the construction of your team page, you have only provided links to the User pages for your team. There are some additional useful links that you could provide for your team's page, what should they be?
  • We encourage you to create a template for your team's useful links.
• The full bibliographic reference needs to be provided for microarray reference 1.
• You have only provided links to the HTML versions of the papers; please provide direct links to the PDF downloads for these articles.
• Microarray reference one is approved for your project (you can comment out the references to the other microarray papers so that they don't appear on the page). You will need to talk to me in class to discuss how to proceed with the data.
  • It appears that there are indeed four biological replicates, not just technical replicates of the samples.
  • Because of some issues with the gene IDs provided on the microarray chip, you may opt to use the following paper for your journal club instead of the one you found in your literature search:
    • Carlson, J.H. et al. (2005) Comparative Genomic Analysis of Chlamydia trachomatis Oculotropic and Genitotropic Strains Infect. Immun. 73: 6407-6418.

— Kdahlquist (talk) 14:41, 4 November 2013 (PST)

Additional Week 10 Notes

• As I mentioned to you in class today, the strain of Chlamydia from which the IDs on the microarray are taken (Olmsland et al. paper) is a different strain than the reference strain for which you found your original genome paper.
  • The reference strain is: Chlamydia trachomatis (strain D/UW-3/Cx) with a taxonomic ID of 272561.
  • The strain used for the gene IDs on the chip is: Chlamydia trachomatis serovar A (strain HAR-13 / ATCC VR-571B) with a taxonomic ID of 305277.
• You may choose to do your journal club on either strain, but for your project to work, you need to match the UniProt and GOA downloads with the microarray chip IDs.

— Kdahlquist (talk) 16:27, 5 November 2013 (PST)

File Naming Convention

Please use the following format in naming all of the files that you work with <Descriptive term(s)>_v<version number>_<Initials>_<yyyymmdd>

• For example: UniProt_v1_KS_201312107

Ksherbina (talk) 09:44, 7 November 2013 (PST)