Similar Datasets
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.
2010-06-11 | GSE19469 | GEO
Project description:We describe a total 222.19 Gb of pig RNA-seq sequences generated from the 18 libraries
2018-02-16 | GSE106381 | GEO
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
Project description:Three-week-old chickens were inoculated with low pathogenic H5N3 AIV and tissues were harvested 4 d pos tinoculation. Four lung cDNA libraries (1 library each for infected and noninfected Leghorn, and infected and noninfected Fayoumi) were prepared and sequenced by Illumina Genome Analyzer II, which yielded a total of 116 million, 75-bp single-end reads.M-BM- The objective of this study was to identify genes and signal pathways associated with resistance to AIV infection in 2 genetically distinct highly inbred chicken lines (Fayoumi, relatively resistant to AIV infection, and Leghorn, susceptible to AIV infection).
2014-05-28 | E-GEOD-57616 | biostudies-arrayexpress
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.
2015-05-14 | GSE54118 | GEO
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 0.395 to 0.740.
2015-05-14 | GSE54117 | GEO
Project description:We present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long-reads and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from three different tissue types from three other species of squid species (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated 33,406 protein coding genes supported by evidence and the genome completeness estimated by BUSCO reached 92%. Repetitive regions cover 49.17% of the genome.
2019-12-16 | PXD016522 | Pride
Project description:Guangxi chickens play a crucial role in promoting the high-quality development of the broiler industry in China, but their value and potential are yet to be discovered. To determine the genetic diversity and population structure of Guangxi indigenous chicken, we analyzed the whole genomes of 185 chickens from 8 phenotypically and geographically representative Guangxi chicken breeds, together with 12 RJFt, 12 BRA and 12 WL genomes available from previous studies. Calculation of heterozygosity (Hp), nucleotide diversity (π), and LD level indicated that Guangxi populations were characterized by higher genetic diversity and lower differentiation than RJFt and commercial breeds except for HGFC. Population structure analysis also confirmed the introgression from commercial broiler breeds. Each population clustered together while the overall differentiation was slight. MA has the richest genetic diversity among all varieties. Selective sweep analysis revealed BCO2, EDN3 and other candidate genes had received strong selection in local breeds. These also provided novel breeding visual and data basis for future breeding.
| S-EPMC8923445 | biostudies-literature
Project description:In this study, methylated DNA immunoprecipitation and high-throughput sequencing (MeDIP-seq) was used to provide an atlas of DNA methylomes in the heart tissue of hypoxic highland Tibetan and lowland Chahua chicken embryos.A total of 31.2 gigabases (Gb) of sequence data were generated from six MeDIP-seq libraries. We identified 1049 differentially methylated regions (DMRs) and 695 related differentially methylated genes (DMGs) between the two chicken breeds. The DMGs were involved in vascular smooth muscle contraction, VEGF signaling pathway, calcium signaling pathway, and other hypoxia related pathways. Five candidate genes that had low methylation (EDNRA, EDNRB, BMPR1B, BMPRII, and ITGA2) might have key regulatory functions for hypoxia adaptation in Tibetan chicken embryos. Our study provides significant explanations for the functions of genes and their epigenetic regulation for hypoxic adaptation in Tibetan chickens.
2017-05-23 | GSE99129 | GEO
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