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Gallus gallus

ABSTRACT: Whole genome sequencing of Ryujin-Jidori and Rhode Island Red chickens

PROVIDER: PRJDB17745 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	DRR539236_1.fastq.gz	Fastqsanger.gz
	DRR539236_2.fastq.gz	Fastqsanger.gz
	DRR539237_1.fastq.gz	Fastqsanger.gz
	DRR539237_2.fastq.gz	Fastqsanger.gz
	DRR539238_1.fastq.gz	Fastqsanger.gz

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An initial map of chromosomal segmental copy number variations in chickens

2010-06-11 | GSE19469 | GEO

An initial map of chromosomal segmental copy number variations in chickens

Project description:Chromosomal segmental copy number variation (CNV) has been recently recognized as a very important source of genetic variability. Some CNV loci involve genes or conserved regulatory regions. Compelling evidence indicates that CNVs impact genome functions. The chicken is a very important farm animal species which has also served as model animal for biological and biomedical research for hundreds of years. A map of CNVs in chickens could facilitate the identification of chromosome regions that segregate for important agricultural and disease phenotypes. NimbleGen 385k whole genome tiling arrays were used to map CNVs in the chicken. This study has identified 96 CNVs in three lines of chickens (broiler, Leghorn and Rhode Island red). These CNVs encompass 16 Mb (1.3%) of the chicken genome. Twenty six CNVs were found in two or more animals. Smaller sized CNVs mostly affect none coding sequences while larger CNV regions involve genes, for example prolactin receptor, aldose reductase and zinc finger proteins, suggesting chicken CNVs potentially affect agricultural or disease related traits. Blood DNA isolated from Cornish Rock, Leghorn and Rhode Island Red birds. Cy5 labeled DNA from a Cornish Rock male used as reference was mixed with Cy3 labeled DNA samples was then hybridized to the 385K chicken tiling array. Fluorescence intensity data were normalized with qspline algorithm and ratio data were analyzed with the circular binary segmentation algorithm from Olshen et al. Copy number variation calls were made if the averaged Log2 ratio of a segment was shifted by 0.3 from the baseline.

2010-06-11 | E-GEOD-19469 | biostudies-arrayexpress

Gallus gallus

Project description:Restriction-site associated DNA sequencing of the Ryujin-Jidori and Rhode Island Red breeds and their F1 and F2 chickens

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Validation experiment of copy number variations identified by next-generation sequencing in chickens (part 2)

Project description:Copy number variation (CNV) is important and widespread in the genome, and is a major cause of disease and phenotypic diversity. Herein, we perform a genome-wide analysis of CNVs in the 12 diversified chicken genomes based on next-generation sequencing. We apply aCGH experiments to confirm our predicted CNVs. Results from aCGH agree well with our findings and the Pearson’s correlation values between the test and reference samples range from 0.644 to 0.722. The whole blood samples from Cornish, Rhode Island Red, and White Leghorn

2015-05-14 | E-GEOD-54118 | biostudies-arrayexpress

Project description:Whole genome resequencing of Rhode Island red chicken

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Affymetrix SNP array data for Dwarf and Rhode Island Red chicken samples

Project description:The genetic foundation of chicken tail feather color is not very well studied to date, though that of body feather color is extensively explored. In the present study, we used a synthetic chicken dwarf line (DW), which was originated from the hybrids between a black tail chicken breed, Rhode Island Red (RIR) and a white tail breed, Dwarf Layer (DL), to understand the genetic rules of the white/black tail color. The DW line still contain the individuals with black or white tails, even if the body feather are predominantly red, after more than ten generation of self-crossing and being selected for the body feather color. We firstly performed four crosses using the DW line chickens including black tail male to female, reciprocal crosses between the black and white, and white male to female to elucidate the inheritance pattern of the white/black tail. We found that (i) the white/black tail feather colors are independent of body feather color and (ii) the phenotype are autosomal simple trait and (iii) the white are dominant to the black in the DW lines. Furtherly, we performed a genome-wide association (GWA) analysis to determine the candidate genomic regions underlying the tail feather color by using black tail chickens from the RIR and DW chickens and white individuals from DW lines.

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Project description:Gallus gallus strain:Rhode Island White hens Genome sequencing

| PRJNA231017 | ENA

Gallus gallus strain:Rhode Island White hens

Project description:Gallus gallus strain:Rhode Island White hens Genome sequencing

| PRJNA231763 | ENA

Gallus gallus strain:Rhode Island White hens

Project description:Gallus gallus strain:Rhode Island White hens Genome sequencing

| PRJNA231758 | ENA

DNA methylation and hydroxymethylation assessment through Illumina EPIC array analysis of paired bisulfite and oxidative-bisulfite conversion

Project description:Analysis of genome-wide hydroxymethylation within infant placenta tissue collected at term. These samples have been collected from the Rhode Island Child Health Study (RICHS) cohort.

2021-01-04 | GSE144129 | GEO

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