|
| Status |
Public on Jul 29, 2008 |
| Title |
before shift, biological rep1 |
| Sample type |
RNA |
| |
|
| Source name |
R. sphaeroides 2.4.1, before shift
|
| Organism |
Cereibacter sphaeroides 2.4.1 |
| Characteristics |
wild type
|
| Treatment protocol |
Total RNA was extracted directly from the culture.
|
| Growth protocol |
R. sphaeroides 2.4.1 was grown in 800 ml of medium in 1-liter glass bottles under anaerobic photosynthesis conditions (bubbled with a gas mixture of 95% N2 and 5% CO2). When the optical density at 600 nm (OD600) reached approximately 0.2 to 0.3, the light was turned off and the composition of the gas mixture was abruptly changed for aerobic growth conditions (gas mixture of 30% O2, 69% N2, and 1% CO2). RNA was isolated from a 50-ml aliquot of the culture prior to the shift to aerobic conditions (0 min) and at 15 min, 30 min, 1 h, 2 h, and 4 h after the shift.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by a modified hot-phenol method described in J. Biol. Chem. 279:9146-9155, 2004
|
| Label |
biotin
|
| Label protocol |
cDNA synthesized from total RNA was fragmented and labeled using the Enzo BioArray terminal labeling kit
|
| |
|
| Hybridization protocol |
Target hybridization, staining, and scanning were performed according to the instructions designed for the Pseudomonas aeruginosa genome array by Affymetrix
|
| Scan protocol |
Agilent GeneArray scanner under the control of the Affymetrix GCOS
|
| Description |
Gene expression data from anaerobic photosynthesis condition, i.e. before shift to aerobic condition
|
| Data processing |
.CEL file converted to MAS5 format and analyzed using Affymetrix MAS5 default analysis settings and global scaling as normalization method.
|
| |
|
| Submission date |
Jul 28, 2008 |
| Last update date |
Jul 29, 2008 |
| Contact name |
Jung Hyeob Roh |
| E-mail(s) |
jung.h.roh@uth.tmc.edu, junghyeob@gmail.com
|
| Phone |
713-500-5437
|
| Organization name |
The University of Texas
|
| Department |
Microbiology & Molecular Genetics
|
| Street address |
6431 Fannin St.
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL162 |
| Series (1) |
| GSE12269 |
Transcriptome dynamics during the transition from anaerobic photosynthesis to aerobic respiration in R. sphaeroides |
|
