Difference between revisions of "Mpetredi Week 10"

Revision as of 04:08, 1 November 2013

Mitchell Petredis

[[Team Name]]

Microarray Papers

PubMed Results

1. Go to [PubMed]
2. Click on [Advanced]
3. 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
4. 3 results appear upon search.
   • [Construction and validation of a Sinorhizobium meliloti whole genome DNA microarray: genome-wide profiling of osmoadaptive gene expression.]
   • [Development of a lab-made microarray for analyzing the genetic diversity of nitrogen fixing symbionts Sinorhizobium meliloti and Sinorhizobium medicae.]
   • [Metabolic capacity of Sinorhizobium (Ensifer) meliloti strains as determined by phenotype MicroArray analysis.]

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

1. Go to [AssayExpress]
2. Click on [Experiments]
3. Type "transcription profiling by array" in the search box
4. Use filter "By Organism" and select Sinorhizobium meliloti
5. Click on "filter"
   • You'll get 33 results, as indicated [here]
6. Click on [Assays] to sort by most to least number of assays.
7. In highest ranking order by number of assays, these are the top 3 results:
   1. [Transcription profiling time series of Sinorhizobium meliloti in response to an osmotic upshift elicited by salt or sucrose] 48 Assays
   2. [A Sinorhizobium meliloti IAA-overproducing strain improves phosphate solubilization and Medicago plant yield] 36 Assays
   3. [Stringent response in S. meliloti] 30 Assays

These results were mostly relevant to what I was looking for, but I only selected the first 3. As I have already found 2 papers I like, these other ones are listed here simply as backups.