|
| Status |
Public on Nov 22, 2013 |
| Title |
Assignment of unknown contigs to chicken microchromosome 16 (GGA16) |
| Organism |
Gallus gallus |
| Experiment type |
Genome variation profiling by genome tiling array
|
| Summary |
Trisomy mapping has long been a powerful means for assigning genes to chicken microchromosome 16 (GGA16). The major histocompatibility complex (MHC-Y, MHC-B) and CD1 genes were previously assigned to GGA16 by trisomy mapping. Here we combined array comparative genomic hybridization (aCGH) with trisomy mapping to investigate unassigned genomic contigs (temporarily assigned to chrUn_random) by the chicken genome sequencing projects for sequences originating from GGA16. We used the Cornell Trisomy chicken line in our study, as this line contains an extra copy of GGA16 and crosses between these individuals generate disomic, trisomic, and tetrasomic GGA16 offspring. Through the analysis of these individuals with aCGH, we compare signal intensities from unknowns to those expected based on copy number, and putatively assign or reject assignment to GGA16 accordingly.
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| |
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| Overall design |
A three-condition experiment, where individuals (n=8) are classified based on their GGA16 content, with a total of 24 individuals. Each individual is either disomic (2X), trisomic (3X) or tetrasomic (4X) for GGA16. This 'loop' design also incorporates a dye swap.
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| Contributor(s) |
Abernathy J, Zhou H |
| Citation(s) |
24336927 |
| |
| Submission date |
Jun 06, 2013 |
| Last update date |
Jan 08, 2014 |
| 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 |
| |
|
| Platforms (1) |
| GPL17254 |
Agilent-028412 CGH chicken array focus on unknown chromosomes |
|
| Samples (24)
|
|
| Relations |
| BioProject |
PRJNA207368 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE47690_RAW.tar |
1.2 Mb |
(http)(custom) |
TAR |
| GSE47690_slide1_1_1.txt.gz |
4.3 Mb |
(ftp)(http) |
TXT |
| GSE47690_slide1_1_2.txt.gz |
4.3 Mb |
(ftp)(http) |
TXT |
| GSE47690_slide1_1_3.txt.gz |
4.3 Mb |
(ftp)(http) |
TXT |
| GSE47690_slide1_1_4.txt.gz |
4.3 Mb |
(ftp)(http) |
TXT |
| GSE47690_slide2_1_1.txt.gz |
4.3 Mb |
(ftp)(http) |
TXT |
| GSE47690_slide2_1_2.txt.gz |
4.3 Mb |
(ftp)(http) |
TXT |
| GSE47690_slide2_1_3.txt.gz |
4.3 Mb |
(ftp)(http) |
TXT |
| GSE47690_slide2_1_4.txt.gz |
4.3 Mb |
(ftp)(http) |
TXT |
| GSE47690_slide3_1_1.txt.gz |
4.2 Mb |
(ftp)(http) |
TXT |
| GSE47690_slide3_1_2.txt.gz |
4.3 Mb |
(ftp)(http) |
TXT |
| GSE47690_slide3_1_3.txt.gz |
4.3 Mb |
(ftp)(http) |
TXT |
| GSE47690_slide3_1_4.txt.gz |
4.3 Mb |
(ftp)(http) |
TXT |
| Processed data included within Sample table |
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