|
| Status |
Public on Jun 20, 2015 |
| Title |
wholeblood_infected_rep5 |
| Sample type |
RNA |
| |
|
| Source name |
peripheral blood, at the beginning of clinical signs
|
| Organism |
Bos taurus |
| Characteristics |
tissue: whole blood
infection status: infected
|
| Treatment protocol |
no treatment was applied on samples. They were stored at -20°C until shipment at the end of the trial. They were transported in refrigerated boxes from Kenya to France, then stored at -°C for several week until RNA extraction.
|
| Growth protocol |
whole blood was collected in Tempus tubes
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared using the Tempus
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the Agilent Low Input Quick Amplification Labelling kit according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with a NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented using the Agilent Gene Expression Hybridization kit, according to the manufacturer's instructions, then hybridized to Agilent Bovine Gene expression microarray (V2) for 17h.
|
| Scan protocol |
Slides were scanned immediately after washing with Agilent Gene Expression wash buffers 1 and 2, according to the manufacturer's instructions. Slides were then scanned on the Agilent C Scanner using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 15µm, Dye channel set to Green and Green PMT set to 100%).
|
| Description |
Gene expression of animal n°757 at the beginning of the clinical signs in whole blood
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1-107_sep09 and Grid: 023647_D_F_20121015) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. We processed paired statistical analyses and compared the differential expression between non-infected and infected status.
|
| |
|
| Submission date |
Jun 19, 2015 |
| Last update date |
Jun 23, 2015 |
| Contact name |
Rodrigues Valérie |
| E-mail(s) |
[email protected]
|
| Phone |
+33467593989
|
| Organization name |
CIRAD
|
| Department |
BIOS
|
| Lab |
CMAEE
|
| Street address |
TA A30/G
|
| City |
Montpellier |
| ZIP/Postal code |
34398 |
| Country |
France |
| |
|
| Platform ID |
GPL11649 |
| Series (1) |
| GSE70059 |
Whole blood transcriptome analysis of Mycoplasma mycoides subsp, mycoides-infected cattle confirms immunosuppression but does not reflect local inflammation |
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