|
| Status |
Public on Nov 22, 2013 |
| Title |
trisomic_GGA16_rep2 |
| Sample type |
genomic |
| |
|
| Source name |
erythrocytes
|
| Organism |
Gallus gallus |
| Characteristics |
gga16 copy: 3X
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Erythrocytes were lysed by a cell lysis buffer and treated overnight with proteinase k. Genomic DNA was then isolated by phenol chloroform and dialyzed against TE buffer (Goto etal., Immunogenetics. 1988;27(2):102-9.)
|
| Label |
Cy5
|
| Label protocol |
All labeling reactions were performed according to the Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol, version 6.3, for enzymatic labeling
|
| |
|
| Hybridization protocol |
All hybridizations were performed according to the Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol, version 6.3, for enzymatic labeling
|
| Scan protocol |
All slides were scanned on an Agilent C scanner using the settings recommended in the Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol, version 6.3, for enzymatic labeling
|
| Description |
Biological replicate 2 of 8 individuals trisomic for GGA16
raw data: slide1_1_2: Cy5
|
| Data processing |
Raw median background and signal intensity information were log2-transformed and normalized by the Scaling and Centering method in R-bioconductor. The normalized data were then processed by mixed model ANOVA in SAS, where individuals were analyzed by GGA16 copy (2X, 3X, 4X) to generate LSmeans, fold ratios, and p-values.
|
| |
|
| Submission date |
Jun 06, 2013 |
| Last update date |
Nov 22, 2013 |
| Contact name |
Jason Abernathy |
| Organization name |
USDA-ARS
|
| Lab |
Aquatic Animal Health Research Unit
|
| Street address |
990 Wire Road
|
| City |
Auburn |
| State/province |
AL |
| ZIP/Postal code |
36832 |
| Country |
USA |
| |
|
| Platform ID |
GPL17254 |
| Series (1) |
| GSE47690 |
Assignment of unknown contigs to chicken microchromosome 16 (GGA16) |
|
