|
| Status |
Public on Nov 01, 2015 |
| Title |
compare WT/mutant NC-B |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
NCTC mutant R
|
| Organism |
Staphylococcus aureus subsp. aureus NCTC 8325 |
| Characteristics |
genotype/variation: dapto R
strain: NCTC8325
genotype/variation: wildtype
|
| Treatment protocol |
RNA Protect (Qiagen)
|
| Growth protocol |
S. aureus strains were grownup to OD600=0.8 in MHB (Becton Dickinson) enriched with 1.25 mM CaCl2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Briefly, bacteria were stabilized in RNA protect for 5 minutes, then harvested. Cells were lysed in the presence of 600 µg/ml lysostaphin and total RNA was extracted using the PrestoSpin R bug Kit including DNase I treatment (Molzym). Quantity and absence of contaminating DNA was measured by using the Nanodrop spectrophotometer (Nanodrop Technologies), and by qPCR, respectively.
|
| Label |
cyanine 3
|
| Label protocol |
Incorporation of cyanine dye during reverse transcription
|
| |
|
| Channel 2 |
| Source name |
NCTC wild type
|
| Organism |
Staphylococcus aureus subsp. aureus NCTC 8325 |
| Characteristics |
strain: NCTC8325
|
| Treatment protocol |
RNA Protect (Qiagen)
|
| Growth protocol |
S. aureus strains were grownup to OD600=0.8 in MHB (Becton Dickinson) enriched with 1.25 mM CaCl2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Briefly, bacteria were stabilized in RNA protect for 5 minutes, then harvested. Cells were lysed in the presence of 600 µg/ml lysostaphin and total RNA was extracted using the PrestoSpin R bug Kit including DNase I treatment (Molzym). Quantity and absence of contaminating DNA was measured by using the Nanodrop spectrophotometer (Nanodrop Technologies), and by qPCR, respectively.
|
| Label |
cyanine 5
|
| Label protocol |
Incorporation of cyanine dye during reverse transcription
|
| |
|
| |
| Hybridization protocol |
A mixture of cDNA obtained from reverse transcription of RNA from WT or mutant strains were 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 |
NCTC parental strain
|
| Data processing |
Local background-subtracted signals were corrected for unequal dye incorporation or unequal load of labelled product. Per chip and per spot normalisation wee performed in GeneSpring (7.3)
|
| |
|
| Submission date |
Sep 13, 2013 |
| Last update date |
Nov 01, 2015 |
| Contact name |
FRANCOIS Patrice |
| E-mail(s) |
patrice.francois@genomic.ch
|
| 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) |
| GSE50842 |
In vitro transcriptomic comparison of daptomycin-resistant Staphylococcus aureus |
|
