Jwoodlee Week 10 - Revision history

Jwoodlee: /* Annotated Bibliography of Genomics Papers for your Species */ added answer

2015-11-10T01:12:50Z

‎Annotated Bibliography of Genomics Papers for your Species: added answer

2015-11-10T01:10:30Z

added answer

2015-11-07T00:12:50Z

‎Annotated Bibliography of Genomics Papers for your Species: removed unnecessary language

2015-11-07T00:08:50Z

‎Annotated Bibliography of Genomics Papers for your Species: added advanced search answers

2015-11-06T18:08:34Z

‎Annotated Bibliography of Genomics Papers for your Species: added search results

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 * Drugs(RNA Polymerase Inhibitors) were added to Shigella flexneri in order to see if bacteria became less active.  The control was a group of bacteria with no drugs added to them, and the treatment was a group of bacteria with drugs added to them.
 Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each?
-* There are two drugs RX and RP with 6 samples per drug.  The experiment was run 3 times which yielded 36 assays.  I believe that means 3 biological replicates and 12 technical replicates within each experiment.
+* There are two drugs RX and RP with 6 samples per drug.  The experiment was run 3 times which yielded 36 assays.  I believe that means 3 biological replicates and 12 technical replicates within each experiment, but I am not 100 percent sure.
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 * Drugs(RNA Polymerase Inhibitors) were added to Shigella flexneri in order to see if bacteria became less active.  The control was a group of bacteria with no drugs added to them, and the treatment was a group of bacteria with drugs added to them.
 Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each?
-* There are two drugs RX and RP with 6 samples per drug.  The experiment was run 3 times which yielded 36 assays.  I believe these are all technical replicates of each other.
+* There are two drugs RX and RP with 6 samples per drug.  The experiment was run 3 times which yielded 36 assays.  I believe that means 3 biological replicates and 12 technical replicates within each experiment.
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 Microarray paper:
-The complete bibliographic reference in the APA style (see the Writing LibGuide) You will be using one of three formats, “journal article from database (with DOI), journal article from database (no DOI) or journal article in print (no DOI).)
+The complete bibliographic reference in the APA style:
 *Fu H, Liu L, Zhang X, Zhu Y, Zhao L, Peng J, et al. (2012) Common Changes in Global Gene Expression Induced by RNA Polymerase Inhibitors in ''shigella flexneri''. PLoS ONE 7(3): e33240. doi:10.1371/journal.pone.0033240

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 *#** '''PubMed'''
 *#*** Which advanced search functions were most useful to narrow down the search?  How many results did you get?
-*#****
+*#****I used search by Title/Abstract and used "Shigella Flexneri genome" as my search term.  I got 5 results and they all seemed pretty promising.  Much more effective than the keyword general search.
 *#** '''Google Scholar'''
 *#*** Which advanced search functions were most useful to narrow down the search?  How many results did you get?
-*#****
+*#****"shigella flexneri genome" went into the "all of the words" field, and I made it so the words had to occur in the title of the article. Also, the article had to be published between 1997 and 2010, I chose these dates because I figured that was a realistic range.  I got 8 results in return that were all very good.  The article we ultimately chose was the very first result actually.
 *#** '''Web of Science'''
 *#*** Which advanced search functions were most useful to narrow down the search?  How many results did you get?
-*#****
+*#****I found that searching by title wasn't all that helpful for whatever reason.  For my advanced search I filtered by topic: "shigella flexneri genome" and by title "shigella flexneri" because I figured if it didn't have shigella flexneri in the title it wasn't worth looking for.  Also I filtered the year from 1997-2010 again because that seems like a realistic date.
-−
 Microarray paper:

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 === Annotated Bibliography of Genomics Papers for your Species ===
 *#* Use a keyword search for each of these databases/tools and answer the following:
-*#* I searched the name of the search tool on google and then clicked on the first link in order to access each of these.
+*#* I searched the name of the search tool on google and then clicked on the first link in order to access each of these. For example, I googled "pub med", clicked on the first result, and then entered the following keywords into the search bar on PubMed.
 *#** '''PubMed'''
 *#*** What original keyword(s) did you use?  How many results did you get?
@@ Line 22: / Line 17: @@
 *#****I searched "Shigella Flexneri genome" and got 590 results.
 *#*** Which terms in which combinations were most useful to narrow down the search?  How many results did you get after narrowing the search?
-*#****
+*#****"Shigella Flexneri genome complete" narrowed down the search to 147 results, however I feel a lot of results still aren't relevant, with advanced searching I feel like I could be more effective.
 *#* Use the advanced search functions for each of these three databases/tools and answer the following:
 *#** '''PubMed'''