|
| Status |
Public on Aug 31, 2013 |
| Title |
milk fat globule, goat 4, 24h PI |
| Sample type |
RNA |
| |
|
| Source name |
milk fat globule, goat 4, 24h PI
|
| Organism |
Capra hircus |
| Characteristics |
animal: 4
time (hrs): 24
sample type: milk fat globule
infection: S. aureus
|
| Treatment protocol |
Injection of S. aureus DV137 (10^3 CFU/mL) in the left udder of goats, sampling of milk every 6hrs after injection
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using method with Phenol/chloroform with (Trizol, Invitrogen). Quantification was performed using a spectrophotometer (NanoDrop Technologies) and RNA quality was assessed using Agilent bioanalyzer 2100 slide.One hundred and twenty ng of RNA were converted to labelled cRNA with Cy3 using Agilent procedure.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from120 ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with Agilent bioanalyzer 2100.
|
| |
|
| Hybridization protocol |
300 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in 25X fragmentation buffer following the manufacturers instructions. Fragmented and labelled cRNA samples were diluted in 2X GEx Hybridisation Buffer Hi-RPM and hybridised on the 15K ovine microarray for 17 hours at 60°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 8x15k array slides.
|
| Description |
Gene expression in MFG 24h after S.aureus injection in the mammary gland
MilkFatGlobule_4S_T4
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 10.5 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 019921_D_F_20110821) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
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| |
|
| Submission date |
Jul 12, 2012 |
| Last update date |
Aug 31, 2013 |
| Contact name |
Pauline Marie Brenaut |
| E-mail(s) |
[email protected]
|
| Organization name |
INRA
|
| Street address |
Domaine de Vilvert
|
| City |
Jouy en josas |
| ZIP/Postal code |
78350 |
| Country |
France |
| |
|
| Platform ID |
GPL10427 |
| Series (1) |
| GSE39315 |
Contribution of the mammary epithelial cell to the immune response during early stages of a bacterial infection to Staphylococcus aureus in goats |
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