Axiom Genome-Wide Chicken Array of Broiler Chickens
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ABSTRACT:
PROVIDER: PRJNA544709 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:DNA was isolated from whole red blood cells from various lines and crosses of broiler chickens. DNA was genotyped using Axiom genome-wide chicken array and cel files were analyzed using Axiom Analysis Suite Software (version 3.0.1) with Gallus gallus 5.0 using the software's Best Practices for agricultural animals. The results were exported (Genotyping_Data-3-21-2018.vcf) for all genotype calls and text file of all SNPs with >= 97% call rate rate was also produced for filtering the VCF file (ALL_SNPSs_with_Call_Rate_97_Plus_3-21-2018).
2019-05-25 | GSE131764 | GEO
Project description:To determine the host response to AIV in chicken lungs, a whole chicken genome array was used to analyze RNA isolated from chicken lungs infected with AIV (4dpi) or medium control (NS). Dual-color, direct comparisons were carried between AIV infected and non-infected controls. Each comparison includes four biological replicates. There were 508 mRNAs (347 down-regulated) were differentially expressed following AIV infection. From the results, MX1, IL-8, IRF-7, TNFRS19 are identified as strong candidate genes involved in regulating the host response to AIV infection in the lungs of broiler chickens. Further gene specific knock-down assay is warranted to elucidate underlying mechanism of AIV infection regulation in the chicken.
2012-06-07 | GSE38197 | GEO
Project description:The process of commercial catching, transport and slaughter (CTS) is known to be an acute stressful event in broiler chickens. Corticosteroid concentrations increase, impacting measures of IGF-1, growth hormone and metabolites of the immune system from blood plasma samples. We used ARK-Genomics chicken 20K oligo array, a two channel DNA microarray, to investigate the significantly differentially expressed genes in the livers of chickens during CTS.
2010-03-19 | GSE20953 | GEO
Project description:Osteoporosis is a major problem for the laying hen industry due to welfare issues and economic losses related to bone fractures. The objective of this research was to better understand genetic influences on bone integrity by comparing gene expression profiles from bone marrow of chickens expressing phenotypic differences for a number of bone characteristics. Global expression profiles of genes included on the Fred Hutchinson Cancer Research Center (FHCRC) Chicken 13K array were assessed in broiler and layer chickens. Keywords: Gene expression comparison between two chicken lines at 15 weeks of age
2007-01-01 | GSE6268 | GEO
Project description:Osteoporosis is a major problem for the laying hen industry due to welfare issues and economic losses related to bone fractures. The objective of this research was to better understand genetic influences on bone integrity by comparing gene expression profiles from bone marrow of chickens expressing phenotypic differences for a number of bone characteristics. Global expression profiles of genes included on the Fred Hutchinson Cancer Research Center (FHCRC) Chicken 13K array were assessed in broiler and layer chickens. Keywords: Gene expression comparison between two chicken lines at 60 weeks of age
2007-01-01 | GSE6270 | GEO
Project description: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.
2016-02-11 | GSE44440 | GEO
Project description:Optimization of broiler chicken breast muscle protein accretion is key for the efficient production of poultry meat, whose demand is steadily increasing. In a context where antimicrobial growth promoters use is being restricted, it is important to find alternatives as well as to characterize the effect of immunological stress on broiler chicken growth. Despite of its importance, research on broiler chicken muscle protein dynamics has been mostly limited to the study of mixed protein turnover. The present study aims to characterize the effect of a bacterial challenge and the feed supplementation of a citrus and a cucumber extract on broiler chicken individual breast muscle proteins fractional synthesis rates (FSR) using a recently developed dynamic proteomics pipeline. 21 day-old broiler chickens were administered a single 2H2O dose before being culled at different timepoints. A total of 60 breast muscle protein extracts from five experimental groups (Unchallenged, Challenged, Control Diet, Diet 1 and Diet 2) were analyzed using a DDA proteomics approach. Proteomics data was filtered in order to reliably calculate multiple proteins FSR making use of a newly developed bioinformatics pipeline. Broiler breast muscle proteins FSR uniformly decreased following a bacterial challenge, this change was judged significant for 15 individual proteins, the two major functional clusters identified as well as for mixed breast muscle protein. Citrus or cucumber extract feed supplementation did not show any effect on the breast muscle protein FSR of immunologically challenged broilers. The present study has identified potential predictive markers of breast muscle growth and provided new information on broiler chicken breast muscle protein turnover which could be essential for improving the efficiency of broiler chicken meat production.
2024-04-04 | PXD044325 | Pride
Project description:To determine the host response to AIV in chicken lungs, a whole chicken genome array was used to analyze RNA isolated from chicken lungs infected with AIV (4dpi) or medium control (NS). Dual-color, direct comparisons were carried between AIV infected and non-infected controls. Each comparison includes four biological replicates. There were 508 mRNAs (347 down-regulated) were differentially expressed following AIV infection. From the results, MX1, IL-8, IRF-7, TNFRS19 are identified as strong candidate genes involved in regulating the host response to AIV infection in the lungs of broiler chickens. Further gene specific knock-down assay is warranted to elucidate underlying mechanism of AIV infection regulation in the chicken. Dual-color, common reference comparisons were carried between AIV infected and non-infected controls. Four biological replicates, with dye swap labeling, were included in the comparisons. Background subtracted signal intensity were collected from 4 arrays and normalized before data analysis.
2012-06-06 | E-GEOD-38197 | biostudies-arrayexpress
Project description:The process of commercial catching, transport and slaughter (CTS) is known to be an acute stressful event in broiler chickens. Corticosteroid concentrations increase, impacting measures of IGF-1, growth hormone and metabolites of the immune system from blood plasma samples. We used ARK-Genomics chicken 20K oligo array, a two channel DNA microarray, to investigate the significantly differentially expressed genes in the livers of chickens during CTS. We investigate the differences of gene expression profiles in hepatic tissues between control birds (n=10) and birds experiencing CTS (n=10) using an ARK-Genomics chicken 20K oligo array, a two channel DNA array (http://www.ark-genomics.orgmicroarray) with full dye swap.
2010-05-05 | E-GEOD-20953 | biostudies-arrayexpress
Project description: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. 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.
2016-02-11 | E-GEOD-44440 | biostudies-arrayexpress