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Series GSE47690 Query DataSets for GSE47690
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.
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.
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)
GSM1154804 trisomic_GGA16_rep1
GSM1154805 tetrasomic_GGA16_rep1
GSM1154806 tetrasomic_GGA16_rep2
BioProject PRJNA207368

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

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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