|
| Status |
Public on Feb 19, 2016 |
| Title |
strain CV571, mock treatment, rep 3 |
| Sample type |
RNA |
| |
|
| Source name |
Enterococcus faecium
|
| Organism |
Enterococcus faecium |
| Characteristics |
sample: Whole cell
strain: CV571 (pbfF ponA)
agent: Mock
growth phase: exponential phase
|
| Treatment protocol |
An equal volume of ice cold acetone:ethanol (1:1) was added to inactivate bacterial ribonucleases
|
| Growth protocol |
E. faecium strain CV571 (pbfF ponA) was grown to mid-exponential phase (Optical Density 600nm of 0.4 to 0.5) in Brain-Heart Infusion broth at 37C with aeration (200 rpm in a rotary shaker). Cells were then continued to grow for 30 min during either: 1. mock conditions (37C at 200 rpm in an orbital shaker) or 2. penicillin challenge conditions (10 micrograms per milliliter; 37C at 200 rpm in an orbital shaker).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Culture samples were mechanically disrupted in a Biospec Beadbeater using 0.5 mm RNase-free zirconium oxide beads. Following disruption, total bacterial RNA was purified using a Qiagen Rneasy Mini kit.
|
| Label |
Biotin
|
| Label protocol |
10 micrograms of each sample was labeled per Affymetrix (Santa Clara, CA) instructions for prokaryotic arrays (reverse transcribed, DNase I fragmentation and 3' biotinylated).
|
| |
|
| Hybridization protocol |
1.5 ug of RNA were hybrized for 16 hr at 45C on an E. faecium Affymetrix GeneChip. GeneChips were washed and stained in an Affymetrix Fluidics Station using ProKaryotic GE-wash2 protocol.
|
| Scan protocol |
GeneChips were scanned in an Affymetrix 7G GeneArray Scanner
|
| Description |
Gene expression data from mock treated E. faecium strain CV571
|
| Data processing |
The data were analyzed with Microarray Suite version 5.0 using Affymetrix default analysis settings.
|
| |
|
| Submission date |
Feb 01, 2016 |
| Last update date |
Feb 19, 2016 |
| Contact name |
Paul Dunman |
| E-mail(s) |
paul_dunman@urmc.rochester.edu
|
| Phone |
585-276-5700
|
| Organization name |
University of Rochester
|
| Department |
Microbiology and Immunology
|
| Street address |
601 Elmwood Avenue
|
| City |
Rochester |
| State/province |
NY |
| ZIP/Postal code |
14642 |
| Country |
USA |
| |
|
| Platform ID |
GPL21391 |
| Series (1) |
| GSE77436 |
Emergence of cephalosporin resitance in cephalosporin-sensitive class A penicillin binding protein mutants in Enterococcus faecium |
|
