|
| Status |
Public on Oct 01, 2011 |
| Title |
E.coli O157:H7 and B. longum_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
E. coli O157:H7 and B. longum invitro coculture
|
| Organism |
Escherichia coli |
| Characteristics |
strain(s): Escherichia coli o157: H7 and Bifidobacterium longum
culture condition: invitro coculture
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the RNAprotect™ Bacteria Reagent Kit, in accordance with the manufacturer’s protocol (Qiagen, Valencia, CA). Aliquots of approximately 10 ug of isolated RNA were treated with 5 units of RNase-free DNase (Ambion, Austin, TX) for 30 min at room temperature. A Qiagen RNeasy MinElute Kit (Qiagen) was used to purify DNase-treated total RNA, removing degraded DNA, tRNA, rRNA, DNase, contaminating proteins, and potential inhibitors of the reverse transcription reaction.
|
| Label |
biotin
|
| Label protocol |
One-Cycle Target Labeling and Control Reagents
|
| |
|
| Hybridization protocol |
Affymetrix standard procedures
|
| Scan protocol |
using GeneChip Scanner 3000
|
| Description |
O157 and BL were pre-cultured for overnight anaerobically. In monoculture, BL and O157 were inoculated 1% individually for the labeling medium in 100-mL serum vials and cultured at 37°C. In coculture, pre-cultured O157 was inoculated 1% for the labeling medium and cultured at 37°C. After 1 hr, pre-cultured BL was inoculated 1% for O157 culture medium and cultured at 37°C. These cultures were stopped at the mid-exponential phase (OD600 = 1.0) and centrifuged for 10 min at 15,000 rpm and the supernatants were removed.
|
| Data processing |
GeneSpring version 7.3.1 (Agilent software) was used for RMA normalization.
|
| |
|
| Submission date |
Oct 08, 2009 |
| Last update date |
Oct 01, 2011 |
| Contact name |
Shinji Fukuda |
| E-mail(s) |
sfukuda@sfc.keio.ac.jp
|
| Organization name |
Keio University
|
| Department |
Institute for Advanced Biosciences
|
| Lab |
Microbiome Research Group
|
| Street address |
246-2 Mizukami, Kakuganji
|
| City |
Tsuruoka |
| State/province |
Yamagata |
| ZIP/Postal code |
997-0052 |
| Country |
Japan |
| |
|
| Platform ID |
GPL3154 |
| Series (1) |
| GSE18474 |
A novel metabolic monitoring system identified nutrition-mediated microbial interactions |
|
