|
| Status |
Public on Apr 03, 2009 |
| Title |
Infested Holstein 3 |
| Sample type |
RNA |
| |
|
| Source name |
Skin biopsy
|
| Organism |
Bos taurus |
| Characteristics |
gender: female
age: 6 months
tissue: skin
disease state: heavy challenge with R.microplus
genotype: Holstein-Friesian
|
| Treatment protocol |
N/A
|
| Growth protocol |
Whole skin tissue sample (8 mm diameter and 10 mm deep) obtained with biopsy punch, no growth protocol or treatment
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Skin tissue frozen in liquid nitrogen, wrapped in heavy duty aluminium and pulverised with hammer on metal block at -80°C. Returned to LN2. Pulverised tissue transferred to 1500 μl chilled Trizol reagent (Invitrogen) with four small glass beads and homogenised in tissue homogeniser for 1 min, returned to ice. Total RNA extracted using protocol for Trizol reagent as per manufacturer's instructions. RNA resuspended in 30 μl RNase-free H20 and treated with 0.75 μl Turbo DNase (Ambion) according to the manufacturer's instructions. RNA sample cleaned with RNeasy mini columns (Qiagen) and eluted from column in 50 μl RNase-free H20.
|
| Label |
biotin
|
| Label protocol |
As per GeneChip expression manual, performed by the Australian Genome Research Facility
|
| |
|
| Hybridization protocol |
As per GeneChip expression manual, performed by the Australian Genome Research Facility
|
| Scan protocol |
Agilent Microarray Scanner (Agilent Technologies) as per Affymetrix GeneChip manual
|
| Description |
n/a
|
| Data processing |
The data were analyzed with R/Bioconductor using RMA normalization. Additional parameters: background correction was convolution, quantile normalization and summarization with median polish.
|
| |
|
| Submission date |
Mar 23, 2009 |
| Last update date |
Apr 03, 2009 |
| Contact name |
Emily Kate Piper |
| E-mail(s) |
e.piper@uq.edu.au
|
| Organization name |
University of Queensland
|
| Department |
School of Veterinary Science
|
| Street address |
Seddon Buildings (Bldg 82)
|
| City |
Brisbane |
| ZIP/Postal code |
4072 |
| Country |
Australia |
| |
|
| Platform ID |
GPL2112 |
| Series (1) |
| GSE15342 |
Microarray analysis of gene expression in the skin of tick-naïve and tick-infested Holstein-Friesian and Brahman cattle |
|
