|
| Status |
Public on Feb 03, 2013 |
| Title |
LD_Piedmontese_135d |
| Sample type |
RNA |
| |
|
| Source name |
Piedmontese by Hereford LD muscle, 135 days gestation
|
| Organism |
Bos taurus |
| Characteristics |
cross: Piedmontese by Hereford
age: 135 days gestation
tissue: LD muscle
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trizol following the manufacturer's instructions
|
| Label |
Cy3, Cy5
|
| Label protocol |
Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential
|
| |
|
| Hybridization protocol |
Scanned on an Agilent G2565AA scanner.
|
| Scan protocol |
Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).
|
| Description |
Sample: P135
Sample replicates: P135_1, P135_2, P135_3
Raw files are listed in 'README_SampleReps_RawFiles_CyDyes.txt' which is linked as supplementary file on the Series record.
|
| Data processing |
Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization. Further, a mixed model normalisation method was applied and the BLUP solution for the gene by condition interaction was used as the normalized mean expression of each gene in each experimental condition.
We used a loop experimental design, and in these cases computing red/green ratios are not optimal. Instead we computed the intensity of the red and the intensity of the green signals.
|
| |
|
| Submission date |
Feb 02, 2013 |
| Last update date |
Feb 03, 2013 |
| Contact name |
Nicholas James Hudson |
| E-mail(s) |
nick.hudson@csiro.au
|
| Phone |
+61 +7 3214 2212
|
| Fax |
+61 +7 3214 2200
|
| Organization name |
CSIRO
|
| Department |
Animal, Food and Health Sciences
|
| Lab |
Systems and Computational Biology
|
| Street address |
306 Carmody Road
|
| City |
Brisbane |
| ZIP/Postal code |
4075 |
| Country |
Australia |
| |
|
| Platform ID |
GPL9712 |
| Series (1) |
| GSE44030 |
Inferring the in vivo cellular program of developing bovine muscle from expression data |
|
