|
| Status |
Public on Jan 01, 2014 |
| Title |
V583 without vancomycin at 10 min_TCR0033 |
| Sample type |
RNA |
| |
|
| Source name |
E. faecalis V583 without vancomycin at 10 min
|
| Organism |
Enterococcus faecalis V583 |
| Characteristics |
agent: without vancomycin
time: 10 min
|
| Growth protocol |
E. faecalis strains were grown in BHI, at 37ºC, until 0.4 OD (600nm). At this point, purified GBAP was added to a final concentration of 10nM in the culture. For others samples we did the same protocol but without GBAP.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was stabilized with RNA protect (Qiagen) and RNA was isolated with RNeasy columns per the manufacturer's instructions (Qiagen). Samples were treated with RNase-free DNase I (Roche) to remove contaminating DNA
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared with the BioArray Terminal Labeling Kit (Enzo Life Sciences).
|
| |
|
| Hybridization protocol |
Samples were hybridized to a previously described custom E. faecalis Affymetrix GeneChip.
|
| Scan protocol |
GeneChips were scanned at the University of Iowa DNA Core Facility.
|
| Description |
Gene expression data from E. faecalis V583 after 10 minutes without vancomycin.
|
| Data processing |
Data was analyzed using Affymetrix GeneChip Operating Software, which identifies probe sets with statistically significant hybridization over background (i.e. presence versus absence calls) and among those, identifies probe sets for which hybridization is significantly increased or decreased in pairwise comparisons of microarray experiments. Signal log ratios for differentially expressed probe sets were averaged and converted to fold change values.
|
| |
|
| Submission date |
Nov 12, 2013 |
| Last update date |
Jan 01, 2014 |
| Contact name |
Neuza Teixeira |
| E-mail(s) |
neuzat@itqb.unl.pt
|
| Organization name |
ITQB
|
| Lab |
Stress by Antibiotics and Virulence of Enterococci
|
| Street address |
Av. da República, Estação Agronómica Nacional
|
| City |
Oeiras |
| ZIP/Postal code |
2780-157 |
| Country |
Portugal |
| |
|
| Platform ID |
GPL16245 |
| Series (1) |
| GSE52263 |
Expression Data from E. faecalis V583 under exposure to 10ug/ml vancomycin |
|
