|
| Status |
Public on Jun 21, 2010 |
| Title |
hypoxic culture-1 |
| Sample type |
RNA |
| |
|
| Source name |
Caulobacter (hypoxic)
|
| Organism |
Caulobacter vibrioides |
| Characteristics |
stress: hypoxia
|
| Treatment protocol |
Two of the four cell batches were subjected to hypoxia at 0.5 OD by sparging the bioreactor with 100% nitrogen gas while maintain robust stirring of the culture. After 20 minutes at 0% dissolved oxygen (as measured by a dissolved oxygen probe), cells were harvested for RNA isolation. Aerated cells were simply harvested at 0.5 OD for RNA isolation (without nitrogen sparge).
|
| Growth protocol |
All batches of cells were intially grown to 0.5 OD in a heavily aerated and pH controlled (pH=7) New Brunswick bioreactor in PYE medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol RNA extraction, followed by DNAseI treatment. RNA was re-extracted using acid phenol, alcohol precipitated, and resuspended in deionized water.
|
| Label |
biotin
|
| Label protocol |
Ten μg of each total RNA was processed to produce single-strand cDNA and RNA was removed using 1N NaOH. cDNA was column purified, fragmented using DNAseI (GE Life Sciences, Piscataway, NJ), and end labeled using GeneChip labeling reagent (Affymetrix, P/N 900542).
|
| |
|
| Hybridization protocol |
Labeled cDNA was hybridized to GeneChip CauloHi1 according to GeneChip Expression analysis technical manual (Affymetrix, Santa Clara, CA).
|
| Scan protocol |
After hybridization for 16 hours at 50°C, arrays were washed using protocol PRO-GE-W52-V3 and stained on a GeneChipFluidics Station (Affymetrix) according to the Genechip Expression analysis technical manual. The arrays were scanned using the Affymetrix Gene Chip Scanner 3000 7G.
|
| Description |
n/a
|
| Data processing |
CEL intensity files were generated by GCOS (Gene Chip Operating Software ) v. 1.4. Intensity values were normalized to a mean target value of 500 in GCOS.
|
| |
|
| Submission date |
Mar 30, 2010 |
| Last update date |
Jun 21, 2010 |
| Contact name |
Sean Crosson |
| E-mail(s) |
crosson4@msu.edu
|
| Phone |
5178845345
|
| Organization name |
Michigan State University
|
| Department |
Dept. Microbiology and Molecular Genetics
|
| Street address |
567 Wilson Rd
|
| City |
East Lansing |
| State/province |
Michigan |
| ZIP/Postal code |
48824 |
| Country |
USA |
| |
|
| Platform ID |
GPL10149 |
| Series (1) |
| GSE21127 |
Measuring the effects of hypoxia on transcription in Caulobacter crescentus |
|
