|
| Status |
Public on Jul 31, 2014 |
| Title |
Ecoli_WT_100uM_KCN_Sample1_TechRep1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Control
|
| Organism |
Escherichia coli |
| Characteristics |
strain: BW25113
|
| Treatment protocol |
Untreated
|
| Growth protocol |
Cells aerobically grown to mid-log phase in MOPS/0.5% glucose at 37C and ~250 RPM.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extracted by hot phenol choloroform folled by Qiagen RNA Midi column.
|
| Label |
Cy3
|
| Label protocol |
Samples were directly labeled by direct incorporation of labeled dCTP.
|
| |
|
| Channel 2 |
| Source name |
KCN
|
| Organism |
Escherichia coli |
| Characteristics |
strain: BW25113
|
| Treatment protocol |
Treated with 100 uM KCN for 5 minutes before harvesting
|
| Growth protocol |
Cells aerobically grown to mid-log phase in MOPS/0.5% glucose at 37C and ~250 RPM.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extracted by hot phenol choloroform folled by Qiagen RNA Midi column.
|
| Label |
Cy5
|
| Label protocol |
Samples were directly labeled by direct incorporation of labeled dCTP.
|
| |
|
| |
| Hybridization protocol |
Samples were hybridized as specified in the Corning UltraGAPS manual. Slides were blocked and washed as specified in the Corning UltraGAPS manual
|
| Scan protocol |
Slides were scanned immediately after washing with a Virtek/BioRad scanner.
|
| Description |
Cells were grown in MOPS media/0.5% glucose and aerobic conditions and treated with KCN
|
| Data processing |
Quantification of the scans were performed with ImaGene (Version 6.0.1; BioDiscovery; El Segundo, CA; www.biodiscovery.com); with the results presented in the associated text files. The normalized data VALUE was generated using LOWESS normalization with rank invariant selection, as implemented in lcDNA (receptor.seas.ucla.edu/lcDNA; Hyduke DR, Rohlin L, Kao KC, Liao JC. 2003 A software package for cDNA microarray data normalization and assessing confidence intervals. OMICS 7(3):227-234.)
|
| |
|
| Submission date |
Aug 11, 2010 |
| Last update date |
Jul 31, 2014 |
| Contact name |
Daniel R Hyduke |
| E-mail(s) |
danielhyduke@gmail.com
|
| Organization name |
Utah State University
|
| Department |
Biological Engineering
|
| Street address |
4105 Old Main Hill ENGR 402S
|
| City |
Logan |
| State/province |
UT |
| ZIP/Postal code |
84322-4105 |
| Country |
USA |
| |
|
| Platform ID |
GPL5113 |
| Series (1) |
| GSE23578 |
Cyanide response in Escherichia coli |
|
