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| | ==Electronic Journal Week 10== | | ==Electronic Journal Week 10== |
| − | *# Each person needs to find two potential journal articles that refer to public microarray data for your species than are different than what your teammates have found. Thus, each team should find either 6 (for a 3-person team) or 8 (for a 4 person team) articles. If you cannot find all six or eight articles, please let the instructors know right away.
| + | #Used the EBI Microarray database. |
| − | *#* The experiments must be measuring '''''gene expression''''' aka '''''transcriptional profiling''''' or '''''transcription profiling by array'''''. Microarrays can also be used for other types of experiments, but these won't be suitable for analysis.
| + | #*[[http://www.pnas.org/content/109/48/19781.full | Developmental stage-specific metabolic and transcriptional activity of Chlamydia trachomatis in an axenic medium]] |
| − | *#* State which database you used (e.g., GoogleScholar, PubMed, ISI Web of Science/Knowledge). It may actually be easier to find the microarray data first and then find the corresponding journal article.
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| − | *#* State what you used as search terms and what type of search terms they were.
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| − | *#* Give an overview of the results of the search.
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| − | *#** How many results did you get?
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| − | *#** Give an assessment of how relevant the results were.
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| − | *#* Record the full bibliographic citation of the relevant papers, formatted according to the [[Guidelines for Literature Citations in a Scientific Paper]].
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| − | *#* Create a link to the HTML version of the journal article on the publisher web site. ''Note that PubMed Central is not an actual publisher web site, but a secondary database of papers.''
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| − | *#* Download the PDF file of the journal article, upload it to the wiki and link to it from your team's home page. ''Note that you can only upload the PDF file to our wiki if there are no copyright restrictions on the article. If there are copyright restrictions, then you will need to provide a link to the download on the publisher site.''
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| − | *#* You must also link to the web site where the microarray data resides.
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| − | *#* Download the microarray dataset file, upload it to the wiki, and link to it on your individual and team pages.
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| − | *#** Remeber, microarray data is not centrally located on the web. Some major sources are:
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| − | *#*** [http://www.ncbi.nlm.nih.gov/geo/ NCBI GEO]
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| − | *#*** [http://www.ebi.ac.uk/microarray-as/ae/ EBI ArrayExpress]
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| − | *#*** [http://smd.princeton.edu/ Stanford Microarray Database]
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| − | *#*** [http://puma.princeton.edu/ PUMAdb (Princeton Microarray Database)]
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| − | *#*** In addition, microarray data can sometimes be found as supplementary information with a journal article or on an investigator's own web site.
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| − | *#** For each of the microarray articles/datasets, answer the following:
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| − | *#**# What experiment was performed? What was the "treatment" and what was the "control" in the experiment?
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| − | *#**# Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each?
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| − | *#* On your team wiki page, compile the list of citations, links, and answers to questions, ranking the papers one through six (or eight) in order of preference for using the dataset for your project. The instructors will review your results to make sure that the data are suitable for the project before you move forward with the analysis.
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