|
| Status |
Public on May 01, 2007 |
| Title |
KT2440(pCAR1)_succinate_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
KT2440(pCAR1)_succinate
|
| Organism |
Pseudomonas putida |
| Characteristics |
Pseudomonas putida KT2440(pCAR1)
|
| Growth protocol |
100 ml of Nitrogen-plus Mineral Medium-4 supplemented with 1.0 mg ml-1 sodium succinate was inoculated by overnight culture in Luria broth to obtain initial optical densities at 600 nm (OD600) of 0.05. Cultures were incubated at 30˚C in a rotating shaker at 120 rpm to exponential phase.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
A total of 1 × 10^9 cells were mixed with RNA Protect Bacteria reagent (Qiagen, Valencia, CA) as recommended by the manufacturer. Total RNA was extracted using the RNeasy Midi kit (Qiagen). The eluted RNA was treated with RQ1 RNase-free DNase (Promega, Madison, WI) at 37˚C for 1 h. After the inactivation of the DNase by the addition of the stop reagent, and subsequent incubation at 65˚C for 15 min, RNA samples were again purified with the RNeasy Mini column according to the manufacturer’s clean-up protocol (Qiagen).
|
| Label |
Cy3
|
| Label protocol |
Samples were labeled by Nimblegen Systems, Inc.
www.nimblegen.com
|
| |
|
| Hybridization protocol |
Hybridization was performed by Nimblegen Systems, Inc.
www.nimblegen.com
|
| Scan protocol |
Scan was performed by Nimblegen Systems, Inc.
www.nimblegen.com
|
| Description |
Exponential phase
|
| Data processing |
Microarray data analysis was performed using the robust multi-array average (RMA) method (Irizarry et al., 2003) based on log2 values of absolute signal intensities for PM probes only.
|
| |
|
| Submission date |
Apr 27, 2007 |
| Last update date |
May 01, 2007 |
| Contact name |
Masatoshi Miyakoshi |
| E-mail(s) |
mmiyakoshi@ige.tohoku.ac.jp
|
| Organization name |
Tohoku University
|
| Department |
Department of Environmental Life Sciences
|
| Lab |
Laboratory of Microbial Genetics
|
| Street address |
Aoba-ku, Katahira, 2-1-1
|
| City |
Sendai |
| State/province |
Miyagi |
| ZIP/Postal code |
980-8577 |
| Country |
Japan |
| |
|
| Platform ID |
GPL5128 |
| Series (1) |
| GSE7650 |
Transcriptional network between pCAR1 and KT2440 chromosome |
|
