Mpetredi Week 10 - Revision history

Mpetredi: added categories

2013-11-21T18:22:55Z

added categories

Mpetredi: /* ArrayExpress */ added note about other paper links

2013-11-01T04:08:26Z

‎ArrayExpress: added note about other paper links

Mpetredi: /* Microarray Papers */ added note about other article

2013-11-01T04:04:54Z

‎Microarray Papers: added note about other article

Mpetredi: /* PubMed Results */ added info on first article

2013-11-01T03:46:38Z

‎PubMed Results: added info on first article

Mpetredi: /* ArrayExpress */ added top 3 results for ArrayExpress

2013-10-31T17:15:24Z

‎ArrayExpress: added top 3 results for ArrayExpress

Mpetredi: /* Microarray Papers */ Added notes about ArrayExpress

2013-10-31T17:09:36Z

‎Microarray Papers: Added notes about ArrayExpress

Mpetredi: fixed an errant link

2013-10-31T03:47:25Z

fixed an errant link

Mpetredi: Added search term guide

2013-10-29T21:49:45Z

Added search term guide

← Older revision		Revision as of 18:22, 21 November 2013
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	{{Individual Assignment Categories}}		{{Individual Assignment Categories}}
		+	[[Category: Sinorhizobium meliloti]]
		+	[[Category: Group Projects]]

@@ Line 30: / Line 30: @@
 ##[[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21745/?keywords=%22Transcription%20profling%20by%20array%22%20&organism=Sinorhizobium%20meliloti&array=&exptype%5B0%5D=&exptype%5B1%5D=&page=1&pagesize=50&sortby=assays&sortorder=descending A Sinorhizobium meliloti IAA-overproducing strain improves phosphate solubilization and Medicago plant yield]] 36 Assays
 ##[[http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-703/?keywords=%22Transcription%20profling%20by%20array%22%20&organism=Sinorhizobium%20meliloti&array=&exptype%5B0%5D=&exptype%5B1%5D=&page=1&pagesize=50&sortby=assays&sortorder=descending Stringent response in S. meliloti]] 30 Assays
 {{Individual Assignment Categories}}

← Older revision		Revision as of 04:04, 1 November 2013
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	The 3 articles from PubMed all seem relevant to what I was searching for. The best article in my opinion, ''Construction and validation of a Sinorhizobium meliloti whole genome DNA microarray: genome-wide profiling of osmoadaptive gene expression'', describes in great detail how they obtained the gene expression of the species via validation of a whole genome DNA microarray. The experiment compare one reference RNA to 2 other RNA cultures, 2 replicate experiments were biological, and 1 replicate was technical.		The 3 articles from PubMed all seem relevant to what I was searching for. The best article in my opinion, ''Construction and validation of a Sinorhizobium meliloti whole genome DNA microarray: genome-wide profiling of osmoadaptive gene expression'', describes in great detail how they obtained the gene expression of the species via validation of a whole genome DNA microarray. The experiment compare one reference RNA to 2 other RNA cultures, 2 replicate experiments were biological, and 1 replicate was technical.
		+
		+	The second best would be the second article, ''Development of a lab-made microarray for analyzing the genetic diversity of nitrogen fixing symbionts Sinorhizobium meliloti and Sinorhizobium medicae''. Like the previous article, it too describes the process of making a microarray for the species to obtain a better idea and comparison of gene expression for two species of Sinorhizobium. According to the article, 3 replicates were performed, but it is not clear as to if they are biological, technical, or a combination of both types of replicates.

	===ArrayExpress===		===ArrayExpress===

@@ Line 13: / Line 13: @@
 #*[[http://www.ncbi.nlm.nih.gov/pubmed/16626823 Development of a lab-made microarray for analyzing the genetic diversity of nitrogen fixing symbionts Sinorhizobium meliloti and Sinorhizobium medicae.]]
 #*[[http://www.ncbi.nlm.nih.gov/pubmed/19561177 Metabolic capacity of Sinorhizobium (Ensifer) meliloti strains as determined by phenotype MicroArray analysis.]]
 ===ArrayExpress===

@@ Line 22: / Line 22: @@
 #*You'll get 33 results, as indicated [[http://www.ebi.ac.uk/arrayexpress/experiments/browse.html?keywords=transcription+profiling+by+array&organism=Sinorhizobium+meliloti&array=&exptype%5B%5D=&exptype%5B%5D= here]]
 #Click on [[http://www.ebi.ac.uk/arrayexpress/experiments/browse.html?keywords=transcription%20profiling%20by%20array&organism=Sinorhizobium%20meliloti&array=&exptype%5B0%5D=&exptype%5B1%5D=&sortby=assays&sortorder=descending Assays]] to sort by most to least number of assays.
+#In highest ranking order by number of assays, these are the top 3 results:
+##[[http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-785/?keywords=%22Transcription%20profling%20by%20array%22%20&organism=Sinorhizobium%20meliloti&array=&exptype%5B0%5D=&exptype%5B1%5D=&page=1&pagesize=50&sortby=assays&sortorder=descending Transcription profiling time series of Sinorhizobium meliloti in response to an osmotic upshift elicited by salt or sucrose]] 48 Assays
 {{Individual Assignment Categories}}

@@ Line 2: / Line 2: @@
 ==Microarray Papers==
 #Go to [[http://www.ncbi.nlm.nih.gov/pubmed?holding=calmulib PubMed]]
 #Click on [[http://www.ncbi.nlm.nih.gov/pubmed/advanced Advanced]]
@@ Line 11: / Line 14: @@
 #*[[http://www.ncbi.nlm.nih.gov/pubmed/19561177 Metabolic capacity of Sinorhizobium (Ensifer) meliloti strains as determined by phenotype MicroArray analysis.]]
 {{Individual Assignment Categories}}

@@ Line 7: / Line 7: @@
 #*Second search term keep as follows: AND, Title, Microarray
 #3 results appear upon search.
-#*[[http://www.ncbi.nlm.nih.gov/pubmed/19561177 Construction and validation of a Sinorhizobium meliloti whole genome DNA microarray: genome-wide profiling of osmoadaptive gene expression.]]
+#*[[http://www.ncbi.nlm.nih.gov/pubmed/?term=Construction+and+validation+of+a+Sinorhizobium+meliloti+whole+genome+DNA+microarray%3A+genome-wide+profiling+of+osmoadaptive+gene+expression Construction and validation of a Sinorhizobium meliloti whole genome DNA microarray: genome-wide profiling of osmoadaptive gene expression.]]
 #*[[http://www.ncbi.nlm.nih.gov/pubmed/16626823 Development of a lab-made microarray for analyzing the genetic diversity of nitrogen fixing symbionts Sinorhizobium meliloti and Sinorhizobium medicae.]]
 #*[[http://www.ncbi.nlm.nih.gov/pubmed/19561177 Metabolic capacity of Sinorhizobium (Ensifer) meliloti strains as determined by phenotype MicroArray analysis.]]

← Older revision		Revision as of 21:49, 29 October 2013
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	{{User Page Link}}		{{User Page Link}}
		+
		+	==Microarray Papers==
		+	#Go to [[http://www.ncbi.nlm.nih.gov/pubmed?holding=calmulib PubMed]]
		+	#Click on [[http://www.ncbi.nlm.nih.gov/pubmed/advanced Advanced]]
		+	#Using the builder, I used MeSH Terms for the first scroll box, followed by "Sinorhizobium meliloti"
		+	#*Second search term keep as follows: AND, Title, Microarray
		+	#3 results appear upon search.
		+	#*[[http://www.ncbi.nlm.nih.gov/pubmed/19561177 Construction and validation of a Sinorhizobium meliloti whole genome DNA microarray: genome-wide profiling of osmoadaptive gene expression.]]
		+	#*[[http://www.ncbi.nlm.nih.gov/pubmed/16626823 Development of a lab-made microarray for analyzing the genetic diversity of nitrogen fixing symbionts Sinorhizobium meliloti and Sinorhizobium medicae.]]
		+	#*[[http://www.ncbi.nlm.nih.gov/pubmed/19561177 Metabolic capacity of Sinorhizobium (Ensifer) meliloti strains as determined by phenotype MicroArray analysis.]]
		+
		+
		+
		+
	{{Individual Assignment Categories}}		{{Individual Assignment Categories}}