|
| Status |
Public on May 01, 2011 |
| Title |
in vivo C57J/B6 plant diet_1 |
| Sample type |
RNA |
| |
|
| Source name |
in vivo gnotobiotic mice fed defined plant diet
|
| Organism |
Bacteroides ovatus |
| Characteristics |
strain: ATCC 8483
treatment: plant diet
isolation source: cecum of C57BL/6 mouse fed defined plant diet
|
| Treatment protocol |
In vitro-grown bacteria or mouse cecal contents were treated with RNAProtect reagent (Qiagen) and frozen at -80C until RNA extraction.
|
| Growth protocol |
Bacteria were grown either in vitro to mid-exponential phase on the defined carbon source indicated; or, extracted from the ceca of gnotobiotic mice colonized with only B. ovatus.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted directly from in vitro-grown bacteria. In vivo-grown cells were subjected to an initial phenol/chloroform bead-beating step. Both types of samples were subjected to final purification steps consisting of Qiagen RNAEasy extraction, Ambicon DNAEasy treatment; Final Qiagen RNAEasy cleanup.
|
| Label |
biotin
|
| Label protocol |
Biotin-UDP end labeling.
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 45C on custom GeneChip GPL9803. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
|
| Description |
16909
|
| Data processing |
The data were analyzed with Affymetrix Expression Console software using default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
|
| |
|
| Submission date |
Nov 23, 2010 |
| Last update date |
May 01, 2011 |
| Contact name |
Eric Charles Martens |
| E-mail(s) |
[email protected]
|
| Phone |
734-647-5800
|
| Organization name |
University of Michigan Medical School
|
| Department |
Dept. of Microbiology and Immunology
|
| Street address |
1150 West Medical Center Drive
|
| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109 |
| Country |
USA |
| |
|
| Platform ID |
GPL9803 |
| Series (2) |
| GSE25575 |
Depolymerization of plant cell wall glycans by symbiotic human gut bacteria (Bacteroides ovatus) |
| GSE25576 |
Depolymerization of plant cell wall glycans by symbiotic human gut bacteria |
|
