|
| Status |
Public on Nov 26, 2012 |
| Title |
treated sample at 30 min, biological rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Escherichia coli MG1655 after 30 min incubation following colicin M treatment
|
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Characteristics |
treatment: treated culture
|
| Treatment protocol |
When the cultures reached an OD600 0.6 they were split into two flasks, each containing 20 ml of the culture. One was treated with a subinhibitory concentration of purified colicin M, while the untreated served as a control. 2-ml culture aliquotes were harvested from each flask after 30 min and 60 min incubation at 37°C and were mixed with 4 ml RNAProtect Bacteria Reagent (Qiagen).
|
| Growth protocol |
Overnight cultures of E. coli MG1655 grown at 37°C with shaking at 200 rpm were diluted 1:625 into 50 ml of LB broth (Roth), and incubated at 37°C with shaking at 200 rpm.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy Mini Kit (Qiagen) according to the manufacturer's protocol.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cDNA were prepared as proposed by the Affymetrix protocol from 10 ug total RNA (GeneChip® Expression Analysis Technical Manual, 2005, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, cDNA were hybridized for 16 hr at 45C in an Affymetrix hybridization oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
|
| Description |
Gene expression data from treated culture following 30 min incubation after reaching OD600 0.6, when exposed to colicin M.
|
| Data processing |
Data were normalized using RMA algorithm from R/Bioconductor/XPS package.
|
| |
|
| Submission date |
Apr 04, 2012 |
| Last update date |
Nov 26, 2012 |
| Contact name |
simona kamensek |
| E-mail(s) |
simona.kamensek@bf.uni-lj.si
|
| Organization name |
university of ljubljana, biotechnical faculty
|
| Department |
department of biology
|
| Street address |
večna pot 111
|
| City |
ljubljana |
| ZIP/Postal code |
1000 |
| Country |
Slovenia |
| |
|
| Platform ID |
GPL3154 |
| Series (1) |
| GSE37026 |
Expression data from control and colicin M treated E. coli MG1655 culture |
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