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Series GSE44440 Query DataSets for GSE44440
Status Public on Feb 11, 2016
Title 244K array Comparative Genomic Hybridization for the characterization of CNVs among inbred Fayoumi, inbred Leghorn, Line A broiler, and Line B broiler chicken
Organism Gallus gallus
Experiment type Genome variation profiling by genome tiling array
Summary Chromosomal structural variation can cause alterations in gene dosage and gene regulation between genomes. Structural variants producing a change in the number of copies of a genomic region are termed copy number variants (CNVs). CNVs have been demonstrated to have causative effects on both Mendelian and complex traits, including susceptibility to infectious diseases. We are interested in mapping CNVs to domesticated chicken breeds to help determine structural variation between genomes that influences economically important traits. For this study, Fayoumi, Leghorn, Line A broiler and Line B broiler chicken were chosen. Fayoumi and Leghorn chickens were selected as these two breeds harbor different responses certain pathogens like Avian Influenza Virus and coccidiosis; Broiler Line A and Line B indivduals were chosen as they harbor different intestinal colonization loads to the bacterium Campylobacter jejuni. Campylobacter genetic Line A and genetic Line B are from a commercial producer have been previously described as either resistant (Line A) or susceptible (Line B). Highly inbred chicken lines Fayoumi M15.2 (n=6) and Leghorn GHs6 (n=6) and broilers from Line A (n=24 individuals in pools of 4) and Line B (n=24 individuals in pools of 4)were subjected to array Comparative Genomic Hybridization (aCGH). Each sample was normalized to a Red Jungle Fowl reference. CNVs for each individual and between lines were determined. The major goal of this study was to discover and characterize CNVs in chickens to further narrow in on Quantitative Trait Loci (QTLs) affecting disease response.
Overall design For the test DNA in Fayoumi and Leghorn, samples from 6 inbred Fayoumi and 6 inbred Leghorn individuals were used; For the test DNA in the Campylobacter genetic lines, samples from 24 individual broilers of Line A (in pools of 4) and 24 individual broilers of Line B (in pools of 4) were used. For the reference DNA, Red Jungle Fowl line UCD001 was used from a self-self hybridization.
Contributor(s) Abernathy J, Zhou H
Citation(s) 24628374
Submission date Feb 20, 2013
Last update date Apr 21, 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
Platforms (1)
GPL11041 Agilent-019553 Gallus gallus (chicken) Genome CGH Microarray 244K(Feature Number version)
Samples (24)
GSM1085348 lineA-pool2_RJF
GSM1085349 RJF_lineB-pool4
GSM1085350 lineA-pool1_RJF
BioProject PRJNA189977

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE44440_RAW.tar 1.8 Gb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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