|
| Status |
Public on Jan 01, 2011 |
| Title |
BT15333 |
| Sample type |
RNA |
| |
|
| Source name |
wild-type bacteria from C57BL/6 mouse cecum fed plant-rich diet
|
| Organism |
Bacteroides thetaiotaomicron |
| Characteristics |
strain: VPI-5482
genotype: wild-type
isolation source: cecum of C57BL/6 mouse fed plant-rich diet
|
| Treatment protocol |
Total RNA was extracted directly from cecal contents that contained only wild-type or mutant B. thetaiotaomicron.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Phenol/chloroform bead-beating on cecal contents, 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 cRNA were hybridized for 16 hr at 45C on custom Affymetrix GeneChip GPL11169. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
|
| Data processing |
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix 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 16, 2010 |
| Last update date |
Jan 01, 2011 |
| Contact name |
Eric Charles Martens |
| E-mail(s) |
emartens@umich.edu
|
| 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 |
GPL11169 |
| Series (1) |
| GSE25415 |
Transcription analysis of wild-type and chuR Bacteroides thetaiotaomicron genes in the mouse cecum |
|
