|
| Status |
Public on Mar 15, 2013 |
| Title |
30 min KCN 5 mM, 3 replicates - rep3 |
| Sample type |
RNA |
| |
|
| Source name |
cells of C. metallidurans
|
| Organism |
Cupriavidus metallidurans CH34 |
| Characteristics |
time: 30 min
treatment: KCN 5 mM
|
| Growth protocol |
C. metallidurans cultures were grown in Mineral salts medium + 0.2 % Na-gluconate to a cell turbidity of 100 Klett, metal species added, incubated for 10-30 min, then harvest cells by centrifugation for 1' in 2.0 ml Tubes.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNeasy Mini Kit (Qiagen) was used according to the manufacturers manual including on-column DNase digestion. PCR were done to check for DNA contaminations, only RNA was used that did not generate products in the PCR reaction. RNA quality was checked on formamide gels and measured as RIN on Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany).
|
| Label |
Cy3
|
| Label protocol |
Labeling was done by the service providers ImaGenes GmbH (Berlin) or IMGM Laboratories GmbH (Martinsried)
|
| |
|
| Hybridization protocol |
Hybridisation was done by the service providers ImaGenes GmbH (Berlin) or IMGM Laboratories GmbH (Martinsried)
|
| Scan protocol |
Agilent DNA microarray Scanner were used by the service providers ImaGenes GmbH (Berlin) or IMGM Laboratories GmbH (Martinsried)
|
| Data processing |
First, all spots not related to CH34 were removed (e.g. bright and dark corners, bringing it down from 15743 to 15206 spots). Secondly, some oligonucleotides were spotted more than one time (up to four times). In these cases, a mean signal was calculated and assigned to the oligo. 9,735 probes of the 15,207 remains. Normalized signal intensity: The mean intensity of the pixels of the surrounding area was subtracted from the mean density of the pixels of the spots to give the signal strength. Its deviation was half of the sum of both intensity deviations and the distance (D) value the distance between spot and background pixel intensities divided by the sum of the deviations
|
| |
|
| Submission date |
Nov 09, 2012 |
| Last update date |
Mar 15, 2013 |
| Contact name |
Cornelia Große |
| E-mail(s) |
[email protected]
|
| Organization name |
Martin-Luther-University Halle-Wittenberg
|
| Department |
Faculty of Biology/Microbiology
|
| Street address |
Kurt-Mothes-Str.3
|
| City |
Halle/Saale |
| ZIP/Postal code |
06120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16115 |
| Series (1) |
| GSE42199 |
Response of Cupriavidus metallidurans CH34 to different Au-species |
|
