|
| Status |
Public on Jun 09, 2017 |
| Title |
ATCC_0 vs ATCC_BS 2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
mid exponential growth phase cultures
|
| Organism |
Acinetobacter baumannii ATCC 17978 |
| Characteristics |
strain: ATCC
absence (0) or presence (bs) of 0.5% bile salts: 0
|
| Treatment protocol |
The cultures were treated with a bile salt mixture containing 50% each of cholic acid (CA) sodium salt and deoxycholic acid (DCA) sodium salt, at a final concentration of 0,5% (wt/vol), and incubated in a static culture until it reached an optical density of 0,5 (600nm) before samples were removed for RNA extraction.
|
| Growth protocol |
50 ng of the Dnase-treated RNA was obtained from mid exponential growth phase cultures (optical density of 0.5 at 600 nm).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using hot phenol extraction and subjected to DNase I treatment (Invitrogen). Next, the RNA was cleaned on an RNeasy column (Qiagen) following the manufacturer’s mini cleanup protocol
|
| Label |
Cy5
|
| Label protocol |
Two-color microarray-based prokaryote analysis Fair Play III Labeling v1.3 (Agilent)
|
| |
|
| Channel 2 |
| Source name |
mid exponential growth phase cultures
|
| Organism |
Acinetobacter baumannii ATCC 17978 |
| Characteristics |
strain: ATCC
absence (0) or presence (bs) of 0.5% bile salts: BS
|
| Treatment protocol |
The cultures were treated with a bile salt mixture containing 50% each of cholic acid (CA) sodium salt and deoxycholic acid (DCA) sodium salt, at a final concentration of 0,5% (wt/vol), and incubated in a static culture until it reached an optical density of 0,5 (600nm) before samples were removed for RNA extraction.
|
| Growth protocol |
50 ng of the Dnase-treated RNA was obtained from mid exponential growth phase cultures (optical density of 0.5 at 600 nm).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using hot phenol extraction and subjected to DNase I treatment (Invitrogen). Next, the RNA was cleaned on an RNeasy column (Qiagen) following the manufacturer’s mini cleanup protocol
|
| Label |
Cy3
|
| Label protocol |
Two-color microarray-based prokaryote analysis Fair Play III Labeling v1.3 (Agilent)
|
| |
|
| |
| Hybridization protocol |
Microarrays were hybridized and washed according to manufacturer's protocol.
|
| Scan protocol |
Scanned on an Agilent G2505C scanner
|
| Data processing |
Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1)
|
| |
|
| Submission date |
Aug 05, 2016 |
| Last update date |
Jun 09, 2017 |
| Contact name |
Maria Tomas-Carmona |
| E-mail(s) |
ma.del.mar.tomas.carmona@sergas.es
|
| Organization name |
Instituto de Investigación Biomédica de A Coruña (INIBIC) / Complexo Hospitalario Universitario de A Coruña (CHUAC)
|
| Department |
Microbiology Department
|
| Street address |
As Xubias, 84
|
| City |
A Coruña |
| ZIP/Postal code |
15006 |
| Country |
Spain |
| |
|
| Platform ID |
GPL16729 |
| Series (1) |
| GSE85264 |
Bile salts in Acinetobacter baumannii clinical strains with lack of AdeABC efflux pump |
|
