|
| Status |
Public on Nov 16, 2011 |
| Title |
low-milk yield vs high-milk yield biological rep 3, tech rep 1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
quarter of mammary gland
|
| Organism |
Bos taurus |
| Characteristics |
breed: Holstein Friesian
individual/probe/cow number: 618
lactation: low-milk yield IV
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using (RNeasy Mini Kit Qiagen, Germany), separately from quarter of mammary gland according to the manufacturer’s protocol. 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 labeled using Quick Amp Labeling Kit, two color with Cy5 i Cyc 3 (Agilent) according to manufacturer’s protocol.
|
| |
|
| Channel 2 |
| Source name |
quarter of mammary gland
|
| Organism |
Bos taurus |
| Characteristics |
breed: Holstein Friesian
individual/probe/cow number: 676
lactation: high-milk yield IV
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using (RNeasy Mini Kit Qiagen, Germany), separately from quarter of mammary gland according to the manufacturer’s protocol. 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 labeled using Quick Amp Labeling Kit, two color with Cy5 i Cyc 3 (Agilent) according to 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 |
Biological replicate 3 of 4, technical replicate 1 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 14, 2011 |
| Last update date |
Nov 16, 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) |
| GSE33680 |
Comparing gene expression profiles in the mammary glands of high- and low-milk-yield Holstein Friesian cows |
|
