|
| Status |
Public on Dec 02, 2011 |
| Title |
healthy vs coagulase - positive Staphylococci 6 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
quarter of mammary gland
|
| Organism |
Bos taurus |
| Characteristics |
breed: Holstein Friesian
disease state: healthy tissue in 1,2,3,4 lactation
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Rnasy mini kit following manufacturer's instructions Quantity and quality of each RNA sample was estimated by Nanodrop (Nanodrop, USA) and Bioanalyzer (Agilent, USA).
|
| Label |
Cy3
|
| Label protocol |
1000 ng of total RNA was using to labeling reaction with Quick Amp Labeling Kit, Two Color with Cy5 i Cy3 (Agilent ) according to the manufacturer’s protocol
|
| |
|
| Channel 2 |
| Source name |
quarter of mammary gland
|
| Organism |
Bos taurus |
| Characteristics |
breed: Holstein Friesian
disease state: tissue infected with CoPS in 3,4 lactation
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Rnasy mini kit following manufacturer's instructions Quantity and quality of each RNA sample was estimated by Nanodrop (Nanodrop, USA) and Bioanalyzer (Agilent, USA).
|
| Label |
Cy5
|
| Label protocol |
1000 ng of total RNA was using to labeling reaction with Quick Amp Labeling Kit, Two Color with Cy5 i Cy3 (Agilent ) according to the manufacturer’s protocol
|
| |
|
| |
| Hybridization protocol |
Standard Agilent hybridization protocol.
|
| Scan protocol |
Scanned on an Agilent G2565AA scanner.
Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).
|
| Description |
3,4 lactation is a second experimental group consisting of pooled RNA from cow in 3rd and 4th stage of lactation.
Biological replicate 1 of 4, technical replicate 2 of 2
|
| Data processing |
Background correction method normexp was used and followed by loess method for within array normalization. Between array normalization was performed with the Aquantile method. Mean values of channels intensities were taken as an input and a median of background signal for background correction calculations.
|
| |
|
| Submission date |
Nov 29, 2011 |
| Last update date |
Dec 02, 2011 |
| Contact name |
Pawel Lisowski |
| E-mail(s) |
pawel.lisowski@mdc-berlin.de
|
| Phone |
+493094061370
|
| Organization name |
Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association
|
| Street address |
Hannoversche Str. 28
|
| City |
Berlin |
| ZIP/Postal code |
10115 |
| Country |
Germany |
| |
|
| Platform ID |
GPL11648 |
| Series (1) |
| GSE34031 |
Gene expression profilling in bovine mammary gland pathophysiology |
|
