|
| Status |
Public on Feb 11, 2016 |
| Title |
RJF_Leghorn-ind6 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
whole blood
|
| Organism |
Gallus gallus |
| Characteristics |
strain: Red Jungle Fowl
tissue: whole blood
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from whole blood using the Wizard Genomic DNA extraction kit per the manufacturers protocol.
|
| Label |
Cy5
|
| Label protocol |
The Oligonucleotide Array-Based CGH for Genomic DNA Analysis Protocol for enzymatic labeling from Agilent Technologies was followed for labeling.
|
| |
|
| Channel 2 |
| Source name |
whole blood
|
| Organism |
Gallus gallus |
| Characteristics |
strain: White Leghorn
tissue: whole blood
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from whole blood using the Wizard Genomic DNA extraction kit per the manufacturers protocol.
|
| Label |
Cy3
|
| Label protocol |
The Oligonucleotide Array-Based CGH for Genomic DNA Analysis Protocol for enzymatic labeling from Agilent Technologies was followed for labeling.
|
| |
|
| |
| Hybridization protocol |
The Oligonucleotide Array-Based CGH for Genomic DNA Analysis Protocol for enzymatic labeling from Agilent Technologies was followed for hybridization.
|
| Scan protocol |
Either an Agilent G2505B Scanner was used following the manufacturers protocol or a GenePix 4100A scanner was used with settings of 5 µm resolution, a saturation tolerance of 0.005% and PMT adjusted to a ratio of 1 ± 0.05
|
| Description |
Red Jungle Fowl reference compared to Biological replicate 6 of 6 for Leghorn
|
| Data processing |
Feature extraction was performed using either the Agilent Feature Extraction Software or the GenePix software. Images were processed using R-Bioconductor, Agilent Genomic Workbench version 5.0, and Nexus Copy Number software version 6.1. In R-Bioconductor, data was log2-transformed and normalized by Scale and Centering. Log2 ratios were calculated using each sample as the tester to the red jungle fowl as the reference. This normalized data was processed by the two softwares per the company protocols.
|
| |
|
| Submission date |
Feb 20, 2013 |
| Last update date |
Feb 11, 2016 |
| 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 |
GPL11041 |
| Series (1) |
| GSE44440 |
244K array Comparative Genomic Hybridization for the characterization of CNVs among inbred Fayoumi, inbred Leghorn, Line A broiler, and Line B broiler chicken |
|
