|
| Status |
Public on Dec 02, 2011 |
| Title |
Daptomycin suceptible strain WT 5 hours growth replicate 3 |
| Sample type |
mixed |
| |
|
| Channel 1 |
| Source name |
S. aureus 616 WT
|
| Organism |
Staphylococcus aureus |
| Characteristics |
strain: 616
|
| Treatment protocol |
no treatments
|
| Growth protocol |
5 hours growth in Muller-Hinton
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAprotectTM Bacteria Reagent (Qiagen, Hilden, Germany) and immediately incubated on ice. After centrifugation for 10 min at 6.000 x g and 4°C, the supernatant was discarded and the pellet resuspended in 1 ml RLT-buffer (Qiagen) supplemented with 1 % (vol/vol) β-mercaptoethanol. Cells were disrupted in Lysing Matrix E (MP Biomedicals) using a FastPrep®-24 (MP Biomedicals, Solon, OH, USA), followed by cooling on ice for 2 min. After brief centrifugation, the supernatant was purified using RNeasy®Mini Kit. Final treatment with DNase for 1 h at 37°C and again purified with RNeasy®Mini Kit.
|
| Label |
cyanine 3
|
| Label protocol |
Incorporation during reverse transcription
|
| |
|
| Channel 2 |
| Source name |
gDNA pool
|
| Organism |
Staphylococcus aureus |
| Characteristics |
reference: Staphylococcus aureus gDNA mixture
|
| Treatment protocol |
no treatments
|
| Growth protocol |
5 hours growth in Muller-Hinton
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
RNAprotectTM Bacteria Reagent (Qiagen, Hilden, Germany) and immediately incubated on ice. After centrifugation for 10 min at 6.000 x g and 4°C, the supernatant was discarded and the pellet resuspended in 1 ml RLT-buffer (Qiagen) supplemented with 1 % (vol/vol) β-mercaptoethanol. Cells were disrupted in Lysing Matrix E (MP Biomedicals) using a FastPrep®-24 (MP Biomedicals, Solon, OH, USA), followed by cooling on ice for 2 min. After brief centrifugation, the supernatant was purified using RNeasy®Mini Kit. Final treatment with DNase for 1 h at 37°C and again purified with RNeasy®Mini Kit.
|
| Label |
cyanine 5
|
| Label protocol |
Incorporation during reverse transcription
|
| |
|
| |
| Hybridization protocol |
A mixture of RNA from WT or DAPR strains and gDNA pool was diluted in 50 µl Agilent hybridization buffer, and hybridized at a temperature of 60°C for 17 hours in a dedicated hybridization oven.
|
| Scan protocol |
100% PMT using Agilent scanner
|
| Description |
Staphylococcus aureus daptomycin suceptible strain 616 WT versus Staphylococcus aureus gDNA pool
|
| Data processing |
Local background-subtracted signals were corrected for unequal dye incorporation or unequal load of labelled product. The algorithm consisted of a rank consistency filter and a curve fit using the default LOWESS (locally weighted linear regression) method.
|
| |
|
| Submission date |
Apr 14, 2011 |
| Last update date |
Dec 02, 2011 |
| Contact name |
FRANCOIS Patrice |
| E-mail(s) |
[email protected]
|
| Phone |
+41 (0)22 372 93 37
|
| Organization name |
Genomic Research Laboratory
|
| Department |
Service of Infectious Diseases
|
| Lab |
Genomic Research Lab
|
| Street address |
Rue Gabrielle-Perret-Gentil, 4
|
| City |
Geneva |
| State/province |
Ge 4 |
| ZIP/Postal code |
1211 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL7137 |
| Series (1) |
| GSE28632 |
Daptomycin-Resistance Mechanisms in Clinically-Derived Staphylococcus aureus Strains Assessed by a Combined Transcriptomics and Proteomics Approach |
|
