Difference between revisions of "Mpetredi Week 10"
From LMU BioDB 2013
(added name and categories) |
(added categories) |
||
| (8 intermediate revisions by one user not shown) | |||
| Line 1: | Line 1: | ||
| − | {User Page Link} | + | {{User Page Link}} |
| − | {Individual Assignment Categories} | + | |
| + | ==Microarray Papers== | ||
| + | |||
| + | ===PubMed Results=== | ||
| + | |||
| + | #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/?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.]] | ||
| + | |||
| + | 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=== | ||
| + | #Go to [[http://www.ebi.ac.uk/arrayexpress/ AssayExpress]] | ||
| + | #Click on [[http://www.ebi.ac.uk/arrayexpress/experiments/browse.html Experiments]] | ||
| + | #Type "transcription profiling by array" in the search box | ||
| + | #Use filter "By Organism" and select Sinorhizobium meliloti | ||
| + | #Click on "filter" | ||
| + | #*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 | ||
| + | ##[[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 | ||
| + | |||
| + | 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. | ||
| + | |||
| + | {{Individual Assignment Categories}} | ||
| + | [[Category: Sinorhizobium meliloti]] | ||
| + | [[Category: Group Projects]] | ||
Latest revision as of 18:22, 21 November 2013
Contents |
[edit] Mitchell Petredis
[[Team Name]]
[edit] Microarray Papers
[edit] PubMed Results
- Go to [PubMed]
- Click on [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.
- [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.
[edit] ArrayExpress
- Go to [AssayExpress]
- Click on [Experiments]
- Type "transcription profiling by array" in the search box
- Use filter "By Organism" and select Sinorhizobium meliloti
- Click on "filter"
- You'll get 33 results, as indicated [here]
- Click on [Assays] to sort by most to least number of assays.
- In highest ranking order by number of assays, these are the top 3 results:
- [Transcription profiling time series of Sinorhizobium meliloti in response to an osmotic upshift elicited by salt or sucrose] 48 Assays
- [A Sinorhizobium meliloti IAA-overproducing strain improves phosphate solubilization and Medicago plant yield] 36 Assays
- [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.
