Ksherbina Week 10
From LMU BioDB 2013
| Assignment Description | Week 1 | Week 2 | Week 3 | Week 4 | Week 5 | Week 6 | Week 7 | Week 8 | Week 9 | Week 10 | Week 11 | Week 12 | Week 13 | Week 15 |
| Class Journal | Week 1 | Week 2 | Week 3 | Week 4 | Week 5 | Week 6 | Week 7 | Week 8 | Week 9 | |||||
| Individual Journal | Week 2 | Week 3 | Week 4 | Week 5 | Week 6 | Week 7 | Week 8 | Week 9 | Week 10 | Week 11 |
| Other | Week 5: Database Wiki |
| Final Project | Team H(oo)KD Project Page | Journal Club Presentation | Project Individual Journal |
Locate journal article describing C. trachomatis reference genome
- Go to the PubMed site through the link provided in the LibGuide for the class.
- Beneath the search bar at the top of the page, click on the "Advanced" link.
- Create filters for the search:
- In the first blank field, type in the species name: Chlamydia trachomatis.
- In the drop down menu to the left of that first field, select "MeSH Terms".
- In the next blank field, type in the term "genome".
- In the drop down menu to the left of this field, select "Title".
- Click on the "Search" button to search for an article satisfying the filters that were set.
- Go to the last page of the search results. Since you are looking for the first description of the reference genome for the species of interest, the journal article you are looking for will probably be one of the older articles that come up in the search.
- Click on the link of an article that seems promising. If, after reading the abstract, you believe that this is the article that you are looking for, click on one of the links in the top right under "Links to full text" to retrieve the full article.
Locate journal articles that measure gene expression
- Go to the EBI ArrayExpress database.
- Click on "Experiments" in the navigation toolbar toward the top of the website.
- Go to the "By organism" drop down menu in the "Filter Experiments" section. Select the species Chlamydia trachomatis.
- Click on the "Filter" button to locate the microarray datasets on the database for the selected species.
- Click on one of the links in the "Accession" column to go to the page in the database that contains the microarray data for the experiment designated by that accession number. You will be taken to a site that has a table of various information. The title above that table is the name of the journal article published based on the microarray data.
- For example, click on the link "E-GEOD-10199". This takes you to a page titled "E-GEOD-10199 - Glycogen Accumulation in Chlamydia trachomatis is Controlled by its Plasmid Through Regulation of glgA", where the part after the dash is the name of the article to find.
- Note: The data under the accession number E-GEOD-24119 has not been published in a journal.
- Go to the PubMed site through the link provided in the LibGuide for the class.
- Beneath the search bar at the top of the page, click on the "Advanced" link.
- Create filters for the search:
- In the first blank field, type in the species name: Chlamydia trachomatis.
- In the drop down menu to the left of that first field, select "MeSH Terms".
- In the next blank field, type in the term "microarray".
- In the drop down menu to the left of this field, select "Title/Abstract".
- Click on the "Search" button to search for articles meeting the filter criteria.
- Note: None of the articles that appeared in the results included microarray data that will work for this project either as supplementary material or in an external database. Some of the papers used human microarrays while other papers that used C. trachomatis arrays did not give information about accessing the raw microarray data.
