|
| Status |
Public on Dec 10, 2013 |
| Title |
isopentenol_3_2.5hr |
| Sample type |
RNA |
| |
|
| Source name |
E. coli 0.2% isopentenol 2.5 hr
|
| Organism |
Escherichia coli |
| Characteristics |
genotype: E. coli DH1 containing 3 plasmids pMevT(C159A), pMevB, pC9b
treatment: 0.2% isopentenol addition
|
| Treatment protocol |
When the OD reached 0.3, 0.5 mM IPTG was added to all flasks to induce the pathway protein expression. Also at this point, 0.2% v/v isopentenol was added to the 3 test flasks. 2.5 hr later the samples were extracted.
|
| Growth protocol |
E. coli DH1 containing 3 plasmids: pMevT(C159A), pMevB, pC9b, was inoculated to an OD of 0.1 into 250 ml flasks containing 60 ml M9 media and grown at 30 C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were snap frozen in liquid nitrogen and the cells were lysed with 15 mg/ml lysozyme and total RNA was extracted with the Rneasy Mini Kit. DNA was removed with an on-column DNase treatment. RNA integrity was verified with a 2100 Bioanalyzer (Agilent)
|
| Label |
Alexa Fluor 555
|
| Label protocol |
20 ug of total RNA was converted to cDNA and labeled with Alexa Fluor 555 with the Superscript Plus Indirect cDNA labeling kit (Invitrogen)
|
| |
|
| Hybridization protocol |
Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
|
| Scan protocol |
Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| Description |
Biological replicate 3 of 3
|
| Data processing |
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
|
| |
|
| Submission date |
Dec 09, 2013 |
| Last update date |
Dec 10, 2013 |
| Contact name |
Robert Dahl |
| E-mail(s) |
robdahl@berkeley.edu
|
| Organization name |
University of California-Berkeley
|
| Department |
Chemical Engineering
|
| Lab |
Keasling
|
| Street address |
5885 Hollis St, JBEI
|
| City |
Emeryville |
| State/province |
CA |
| ZIP/Postal code |
94608 |
| Country |
USA |
| |
|
| Platform ID |
GPL14649 |
| Series (1) |
| GSE53138 |
Expression profile of E. coli in response to exogenous addition of isopentenol |
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