Difference between revisions of "Class Journal Week 10"
From LMU BioDB 2013
(→Individual Homework) |
|||
| Line 19: | Line 19: | ||
* For our species we need to find a reference genome = the main reference strain | * For our species we need to find a reference genome = the main reference strain | ||
**generally the earliest strain by date is the reference genome | **generally the earliest strain by date is the reference genome | ||
| + | |||
| + | ==Array express== | ||
| + | *this is one of the best databases I've seen in reference to finding array data | ||
| + | *The search can be sorted by organism and the arrays can be sorted by kinds | ||
==Individual Homework== | ==Individual Homework== | ||
Revision as of 17:19, 31 October 2013
Contents |
Class Notes week 10
- To access database pages go through the LMU link
- journal availibility comes through PubMed central if it is funded by the government
Open Access Journals
- Authors submit article to publishers and then pay to have it published
- How well are the quality control standards?
- Copyright rules are in flux
- most databases are public access
Google Scholar
- serves as a key word search
- date order is all over the place
- means things can be out of date
Pubmed
- also serves as a keyword search
- Advanced search= use the meSH terms
- For our species we need to find a reference genome = the main reference strain
- generally the earliest strain by date is the reference genome
Array express
- this is one of the best databases I've seen in reference to finding array data
- The search can be sorted by organism and the arrays can be sorted by kinds
Individual Homework
- I used pubmed for this part of the assignment
- The search terms I used for this were Sinorhizobium Meliloti and genome.
- Most of the results I got were concerned with DNA probes and specific sequences of DNA
- I got 20 results by using this database
- when I used array express I got 25 results by using the search term for the bacteria species Sinorhizobium Meliloti
Citations
- Dual RpoH Sigma Factors and Transcriptional Plasticity in a Symbiotic Bacterium. Barnett MJ, Bittner AN, Toman CJ, Oke V, Long SR. , Europe PMC 22773790
- Transcriptome Profiling Reveals the Importance of Plasmid pSymB for Osmoadaptation of Sinorhizobium meliloti. Dominguez-Ferreras, Ana; Perez-Arnedo, Rebeca; Becker, Anke; Olivares, Jose; Soto, Maria J.; Sanjuan, Juan. The Journal of Bacteriology 188(21):7617 (2006), Europe PMC 16916894
Links
- http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36186/?keywords=&organism=Sinorhizobium+meliloti&array=&exptype[]=&exptype[]=
- http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-785/?keywords=&organism=Sinorhizobium%20meliloti&array=&exptype[0]=&exptype[1]=&sortby=type&sortorder=ascending
Description of the Arrays
- the first array deals with heat Shock. The control for this experiment was stationary phase growth and the variable was the bacteria under "heat shock"
- The array deals with the osmotic upshift ellicited by salt or sucrose. The control in this experiment would be a normal osmotic gradient and the variables would be the gradient when subjected to salt and sucrose
