|
| Status |
Public on Mar 29, 2010 |
| Title |
array Erus 1 |
| Sample type |
RNA |
| |
|
| Source name |
Erus 1
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: HMEC endothelial cells
infection: R. prowazekii Erus strain
|
| Treatment protocol |
Human endothelial cells (HMEC-1 cell line) were infected with R. prowazekii Erus strain (50:1 bacterium-to-cell ratio) for 6 hours at 37°C.
|
| Growth protocol |
Human endothelial cells (HMEC-1 cell line) were cultured in MCDB 131 medium (Gibco) supplemented with 10% of SVF and 1% of L-glutamine
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy Mini kit (Qiagen).
|
| Label |
Cy3
|
| Label protocol |
Labelled cRNA was synthesised from cDNA using T7 RNA polymerase and cyanine 3-labeled CTP (Cy-3) fluorescent dyes with the One-Color Low RNA Input Linear Amplification KitPLUS (Agilent).
|
| |
|
| Hybridization protocol |
as recommanded by the manufacturer
|
| Scan protocol |
Slides were scanned at a 5-µm resolution with a G2505B DNA microarray scanner (Agilent)
|
| Description |
HMEC endothelial cells infected with R. prowazekii Erus strain
|
| Data processing |
Agilent Feature Extractor Software A.9.1.3 was used for image analysis. The microarray grid was automatically placed, outlier spots were flagged and feature intensities and backgrounds were accurately determined.
Further data processing was performed using Resolver software 7.1 (Rosetta Inpharmatics), and its error model-based transformation pipeline was used to map replicate reporters to genes and to normalise inter-array data sets. The fold change (FC) was calculated using pairs Erus vs. Control, Evir vs. Control and Rp22 vs. Control. Only genes that had an absolute FC over 2.0 (p<0.01) for at least one of them were considered to be regulated and kept for further statistical analysis.
|
| |
|
| Submission date |
May 15, 2009 |
| Last update date |
Mar 29, 2010 |
| Contact name |
Yassina Bechah |
| E-mail(s) |
yassina.bechah@univmed.fr
|
| Organization name |
CNRS
|
| Lab |
URMITE
|
| Street address |
27 bd J. Moulin
|
| City |
Marseille |
| ZIP/Postal code |
13005 |
| Country |
France |
| |
|
| Platform ID |
GPL4133 |
| Series (1) |
| GSE16123 |
Multiomics study to identify virulence factors of Rickettsia prowazekii revealed its adaptive mutation capabilities |
|
