|
| Status |
Public on Jan 01, 2010 |
| Title |
WMARS clay fraction rep #2 |
| Sample type |
other |
| |
|
| Source name |
WMARS clay fraction # 2
|
| Organism |
uncultured Acidobacteriota bacterium |
| Characteristics |
genotype: 16S rRNA gene amplicon
source: WMARS clay fraction
|
| Growth protocol |
For E. coli cultures containing the cloned 16S rRNA gene, 2 ml cultures were grown overnight at 37oC. Plasmid DNA was extracted using a Promega SV96 kit and the cloned Acidobacteria rDNA template was PCR amplified in the presence of Cy3-labeled dCTPs and unincorporated label was removed by Centricon spin columns
|
| Extracted molecule |
other |
| Extraction protocol |
For soil samples, total soil DNA was extracted by MoBio soil kit extraction. The soil Acidobacteria rDNA template was PCR amplified in the presence of Cy3-labeled dCTPs and unincorporated label was removed by Centricon spin columns
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| |
|
| Hybridization protocol |
Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
|
| Scan protocol |
Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| Description |
This sample is of the 16S rRNA gene PCR amplified using primer sets 31F (division Acidobacteria-specific) and 1492R (universal)
|
| Data processing |
mean signal intensity of triplicate probes
|
| |
|
| Submission date |
Oct 23, 2009 |
| Last update date |
Oct 27, 2009 |
| Contact name |
Mark R Liles |
| E-mail(s) |
[email protected]
|
| URL |
http://gump.auburn.edu/liles/
|
| Organization name |
Auburn University
|
| Department |
Biological Sciences
|
| Lab |
Liles
|
| Street address |
Rm 316, Rouse Life Sciences Building
|
| City |
Auburn |
| State/province |
AL |
| ZIP/Postal code |
36849 |
| Country |
USA |
| |
|
| Platform ID |
GPL9479 |
| Series (1) |
| GSE18711 |
A phylogenetic microarray targeting 16S rRNA genes from the bacterial division Acidobacteria |
|
