|
| Status |
Public on Jul 19, 2012 |
| Title |
p437C |
| Sample type |
RNA |
| |
|
| Source name |
p437C
|
| Organism |
Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821 |
| Characteristics |
base medium: rich
stressor: 37C
growth_phase: Mid-exponential
genetic variant: wild type
|
| Treatment protocol |
Varying the base medium, or adding inhibitory compounds, or collecting cells in stationary phase instead of in log phase. Two experiments were done with a mutant flocculent strain, strain ZM401 instead of the wild-type strain ZM4.
|
| Growth protocol |
Aerobic batch growth of Zymomonas mobilis strain ZM4 or ZM401 at 30 C. Rich media (ZMRG) contained 25 g/L glucose, 10 g/L yeast extract, and 2 g/L K2PO4, as well as inhibitory compounds as indicated. Minimal media (ZMMG) contained 20 g/L glucose, salts, and vitamins (A. Goodman et al. Applied and Environmental Microbiology 44:496).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Added RNAProtect (Qiagen) and isolated total RNA with RNAeasy mini kit (Qiagen)
|
| Label |
Alexa fluor 555
|
| Label protocol |
prepared first-strand labeled cDNA with SuperScript Plus Indirect cDNA Labeling Module (Invitrogen)
|
| |
|
| Hybridization protocol |
standard Nimblegen protocol
|
| Scan protocol |
standard Nimblegen protocol
|
| Data processing |
quantile normalized the probe intensities to match a standard and averaged the log2 values for each gene. As a standard, we used the average of the log intensities from the first three unstressed rich media experiments (p1ZMRG1,p1ZMRG2,p2ZMRG).
|
| |
|
| Submission date |
Jul 18, 2012 |
| Last update date |
Jul 19, 2012 |
| Contact name |
Morgan N Price |
| E-mail(s) |
morgannprice@yahoo.com
|
| Organization name |
Lawrence Berkeley Lab
|
| Department |
Physical Biosciences Division
|
| Lab |
Arkin group
|
| Street address |
1 Cyclotron Road Mailstop 977-152
|
| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
| |
|
| Platform ID |
GPL15822 |
| Series (1) |
| GSE39466 |
Comparison of gene expression and mutant fitness in Zymomonas mobilis ZM4 |
|
