|
| Status |
Public on Jun 06, 2007 |
| Title |
Colon Specific Pathogen Free rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Colon, SPF IQI male mice, 9 week old
|
| Organism |
Mus musculus |
| Characteristics |
Strain:colon, Gender:male, Age:9-week, Tissue:Colon, Enteric flora status:specific pathogen free
|
| Treatment protocol |
Nine week old mice (n=3) were sacrificed by cervical dislocation and the colon was dissected (the colon was not divided into proximal and distal sections and was treated as a single intestinal section). Tissue destined for RNA extraction were flash-flozen in liquid nitrogen after washing with ice-cold PBS.
|
| Growth protocol |
GF mice were housed in a Trexler-type flexible film isolator in a standard germ free state and screened on a weekly basis for germ-free status by sampling feces sterilely and culturing on MRS-agar plates under aerobic and anaerobic conditions. All the GF, SPF, ex-GF mice were kept in a 12: 12-h light/dark cycle and at a temperature of 22+-2 ºC.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from mice (n = 3 per each group) using TRIzol (Life Technologies, Rockville, TX) and re-purified by RNeasy spin columns (Quiagen, Valencia, CA), according to the manufacturer’s instructions.
|
| Label |
biotin
|
| Label protocol |
The labeled cRNA was prepared from by in vitro transcription (Enzo Biochem, New York, NY)
|
| |
|
| Hybridization protocol |
The labeled cRNA was fragmented, hybridized to MG-U74Av2 array (Affymetrix, Santa Clara, CA) using an Affymetrix fluidics station according to the Affymetrix protocols.
|
| Scan protocol |
GeneChips were scanned with an Affymetrix scanner, according to the Affymetrix protocols.
|
| Description |
Gene expression data from colon of specific pathogen free mice
|
| 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.
|
| |
|
| Submission date |
Jun 04, 2007 |
| Last update date |
Jun 05, 2007 |
| Contact name |
Masahiro Yamamoto |
| E-mail(s) |
[email protected]
|
| Organization name |
Keio University School of Medicine
|
| Department |
Department of Kampo Medicine
|
| Street address |
35 Shinano-machi
|
| City |
Shinjuku |
| State/province |
Tokyo |
| ZIP/Postal code |
160-8582 |
| Country |
Japan |
| |
|
| Platform ID |
GPL81 |
| Series (1) |
| GSE8006 |
Mice with and without enteric flora |
|
