Difference between revisions of "Dwilliams Week 10 assignment"
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==Electronic Journal Week 10== | ==Electronic Journal Week 10== | ||
| − | === | + | ==Locate journal article describing ''Chlamydia trachomatis'' reference genome== |
| + | #Go to the PubMed site through the link provided in the [http://libguides.lmu.edu/BIOL367 LibGuide] for the class. | ||
| + | #*Select the search bar at the top of the page, then click on the "Advanced" link. | ||
| + | #*In the first blank field, type in the species name: ''Chlamydia trachomatis''. | ||
| + | #*In the drop down menu select the option "MeSH Terms". | ||
| + | #*In the next field, type in the term "genome" for the "Title". | ||
| + | #*Click on the "Search" button to proceed to search for an article that satisfies the filters. | ||
| + | #*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 PubMed site through the link provided in the [http://libguides.lmu.edu/BIOL367 LibGuide] for the class. | |
| − | + | #*Click on the "Advanced" link. | |
| − | + | #*In the first blank field, type in the species name: ''Chlamydia trachomatis''. | |
| − | + | #*In the next field, select "MeSH Terms". | |
| − | + | #*In the next field, type in the term "microarray" for "Title/Abstract". | |
| − | + | #*"Search" for articles meeting the filter criteria. | |
| − | + | #*'''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 ''Chlamydia trachomatis'' arrays did not give information about accessing the raw microarray data.''' | |
| − | + | #Group decided to split up the 4 results found in the EBI Microarray database, I chose to do the information for "E-GEOD-39530 - Developmental stage specific metabolic and transcriptional activity of chlamydial elementary bodies and reticulate bodies in an axenic medium" | |
| − | + | #Used the EBI Microarray database. | |
| − | + | #*Selected article: [[http://www.pnas.org/content/109/48/19781.full Developmental stage-specific metabolic and transcriptional activity of Chlamydia trachomatis in an axenic medium]] | |
| − | + | #*[[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39530/?keywords=&organism=Chlamydia+trachomatis&array=&exptype%5B%5D=&exptype%5B%5D= Microarray Data]] | |
| − | * | + | #*Chlamydiae undergo a biphasic developmental cycle characterized by an infectious cell type known as either an elementary body (EB) and an intracellular replicative form called a reticulate body (RB). Chlamydia was incubated under microaerobic conditions to test the differences in preferred energy source between EB's and RB's. |
| − | + | #*There weren't necessarily a "treatment" group and a "control" group. Referencing figure 4, it can be inferred that EB would be considered the "treatment" group because of the way that the ratio was set up, being EB to RB. In this way the RB would be the "control" group as they are looking at the EB population relative to the RB population. | |
| − | + | #*Replicates were performed for the control and treatment in terms of technical replicates; as the article states that "Density gradient-purified EBs and RBs were incubated in quadruplicate in four-well plates..." | |
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Latest revision as of 03:08, 1 November 2013
[edit] Electronic Journal Week 10
[edit] Locate journal article describing Chlamydia trachomatis reference genome
- Go to the PubMed site through the link provided in the LibGuide for the class.
- Select the search bar at the top of the page, then click on the "Advanced" link.
- In the first blank field, type in the species name: Chlamydia trachomatis.
- In the drop down menu select the option "MeSH Terms".
- In the next field, type in the term "genome" for the "Title".
- Click on the "Search" button to proceed to search for an article that satisfies the filters.
- 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.
[edit] Locate journal articles that measure gene expression
- Go to the PubMed site through the link provided in the LibGuide for the class.
- Click on the "Advanced" link.
- In the first blank field, type in the species name: Chlamydia trachomatis.
- In the next field, select "MeSH Terms".
- In the next field, type in the term "microarray" for "Title/Abstract".
- "Search" for articles meeting the filter criteria.
- 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 Chlamydia trachomatis arrays did not give information about accessing the raw microarray data.
- Group decided to split up the 4 results found in the EBI Microarray database, I chose to do the information for "E-GEOD-39530 - Developmental stage specific metabolic and transcriptional activity of chlamydial elementary bodies and reticulate bodies in an axenic medium"
- Used the EBI Microarray database.
- Selected article: [Developmental stage-specific metabolic and transcriptional activity of Chlamydia trachomatis in an axenic medium]
- [Microarray Data]
- Chlamydiae undergo a biphasic developmental cycle characterized by an infectious cell type known as either an elementary body (EB) and an intracellular replicative form called a reticulate body (RB). Chlamydia was incubated under microaerobic conditions to test the differences in preferred energy source between EB's and RB's.
- There weren't necessarily a "treatment" group and a "control" group. Referencing figure 4, it can be inferred that EB would be considered the "treatment" group because of the way that the ratio was set up, being EB to RB. In this way the RB would be the "control" group as they are looking at the EB population relative to the RB population.
- Replicates were performed for the control and treatment in terms of technical replicates; as the article states that "Density gradient-purified EBs and RBs were incubated in quadruplicate in four-well plates..."
