|
| Status |
Public on Jan 28, 2012 |
| Title |
Control-rep2 |
| Sample type |
RNA |
| |
|
| Source name |
LT-ΔfadE
|
| Organism |
Escherichia coli |
| Characteristics |
strain: LT-ΔfadE
expected approximate fatty acids (c12-c20) titer (mg/l culture): 900
|
| Growth protocol |
Single colonies of each strain were inoculated into 5 mL LB media (containing 50 mg/L ampicillin and 30 mg/L chloramphenicol) and incubated at 37C overnight. The overnight cultures were used to inoculate 5 mL minimal media (M9 medium supplemented with 75 mM MOPS, 2 mM MgSO4, 1 mg/L thiamine, 10 nM FeSO4, 0.1 mM CaCl2 and micronutrients including 3 μM (NH4)6Mo7O24, 0.4 mM boric acid, 30 μM CoCl2, 15 μM CuSO4, 80 μM MnCl2, 10 μM ZnSO4, 2% glucos, 50 mg/L ampicillin and 30 mg/L chloramphenicol) and incubated at 37C until OD600 reached 0.8. Production was induced with 1 mM IPTG and cultures were incubated at 37C with shaking for 12h before sampling.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells where rapidly harvested after 12h of induction and frozen in liquid nitrogen. Total RNA was extracted using the RNEasy Mini kit (Qiagen) following lyzozyme treatment. RNA was quantified by spectrophotometry with a Nanodrop ND-1000 (Thermo Scientific) and its integrity verified on a 2100 Bioanalyzer (Agilent).
|
| Label |
Cy3
|
| Label protocol |
Direct Random labeling as previously described in Ouellet et al., BMC Biotechnology 2009, 9:97.
|
| |
|
| Hybridization protocol |
As recommended [NimbleGen Arrays User's Guide - Gene Expression Analysis v.3.0.] simultaneously for all arrays
|
| Scan protocol |
Individual arrays were scanned independently using a GenePix Professional 4200A scanner (Axon Instruments), adjusting the PMT gain for each array as recommended [NimbleGen Arrays User's Guide - Gene Expression Analysis v.3.0.]. Image analysis was performed with the NimbleScan software and features intensities were exported as .pair files
|
| Data processing |
ArrayStar 3.0 (DNASTAR) was used for probe summarization and normalization (RMA algorithm, quantile normalization) and data analysis
|
| |
|
| Submission date |
Jan 27, 2012 |
| Last update date |
Jan 30, 2012 |
| Contact name |
Mario Ouellet |
| Organization name |
Joint BioEnergy Institute
|
| Street address |
5885 Hollis St., 4th Floor
|
| City |
Emeryville |
| State/province |
CA |
| ZIP/Postal code |
94608 |
| Country |
USA |
| |
|
| Platform ID |
GPL14649 |
| Series (1) |
| GSE35392 |
Effect of FadR overexpression in an engineered fatty acid overproducer |
|
