|
| Status |
Public on Oct 01, 2010 |
| Title |
Serotype1_irondepleted_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Actinobacillus pleuropneumoniae 4074 iron depleted
|
| Organism |
Actinobacillus pleuropneumoniae serovar 1 str. 4074 |
| Characteristics |
serotype: serotype 1 (4074)
growth condition: iron depleted
|
| Treatment protocol |
At mid-log phase, the culture was split into two 10 ml portions. Iron-depleted conditions were established in one of the flasks by addition of 300 µM of the iron chelator 2,2'-dipyridyl. After 30 min growth the cultures were harvested.
|
| Growth protocol |
Actinobacillus pleuropneumoniae was grown to mid-log phase (OD660nm 0.6) in brain heart infusion media supplemented with 0.03% NAD at 37°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Mini kit (Qiagen, Hilden, Germany) and the RNAeasy reagent (Ambion, Cambridgeshire, UK) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen) and subsequently by TURBO DNase (Ambion). RNA contration was measured by NanoDrop (Thermo Scientific, Wilmington, DE, USA) and RNA quality was determined by analysis with an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed at the Center for Biological Sequence Analysis at the Technical University of Denmark, Lyngby, Denmark, following the NimbleGen standard operating protocol. See www.nimblegen.com.
|
| |
|
| Hybridization protocol |
Hybridization was performed following their standard operating protocol. See www.nimblegen.com.
|
| Scan protocol |
Scanning was performed at 5 µm resolution using the NimbleGens MS 200 scanner (NimbleGen Systems, Madison, WI, USA).
|
| Description |
Serotype 1
|
| Data processing |
The raw data (.xys file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249). For RMA normalization we have used RGui version 2.9.2 (2009-08-24) (http://cran.r-project.org/bin/windows/base/), using the package Oligo.
|
| |
|
| Submission date |
Sep 30, 2010 |
| Last update date |
Sep 30, 2010 |
| Contact name |
Kirstine Klitgaard |
| E-mail(s) |
kksc@vet.dtu.dk
|
| Phone |
0045 35886265
|
| Organization name |
National Veterinary Institute, Technical University of Denmark
|
| Street address |
Bulowsvej 27
|
| City |
Copenhagen |
| ZIP/Postal code |
1790 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL11003 |
| Series (1) |
| GSE24470 |
Expression analysis of 6 serotypes of Actinobacillus pleuropneumonia during iron deprivation |
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