Gallus gallus
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ABSTRACT:
PROVIDER: PRJNA387392 | ENA |
REPOSITORIES: ENA
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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:Sichuan domestic chicken and Tibetan chicken genome sequencing
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Project description:Adaptation to hypoxia is a complicated and important physiological course for organisms, but the genetic mechanism underlying the adaptation is not fully understood yet. Tibetan Chicken (T), an indigenous chicken breed in China which inhabit in high areas with an altitude above 2,900 meters. Shouguang Chicken(S) and Dwarf Recessive White Chicken (DRW), two lowland chicken breeds, were used as control groups. The heart was the first functional organ to develop during the embryonic development. Furthermore, the heart is an efficient energy converter utilizing the most appropriate fuel for a given environment. Therefore, GeneChip® Chicken Genome Array was employed to identify the differentially expressed genes in embryonic hearts of Tibetan Chicken and two lowland chicken breeds in both hypoxic and normoxic incubating environments with a genome wide profile. Experiment Overall Design: To obtain general expression profiles of embryonic hearts in Tibetan Chicken(T), Dwarf Recessive White Chicken (DRW)and Shouguang Chicken (S)in hypoxia and normoxia, the fertilized full sib eggs of all the three chicken breeds were incubated under two different conditions. The heart was isolated from all the three chicken breeds under the two different conditions for RNA extraction and hybridization on Affymetrix microarrays.
2009-09-17 | E-GEOD-12675 | biostudies-arrayexpress
Project description:Copy number variation profiles comparing control female Dehong chiken blood DNA with 11 different chicken breeds(Silkie, Tibetan Chicken, Gallus gallus spadiceus, Bearded Chicken, Jinhu Chicken, Anak Chicken, Beijing Fatty Chicken, Langshan Chicken, Qingyuan partridge Chicken, Shek-Ki Chicken, Wenchang Chicken) blood DNA. Each test breeds had one male and one female sample, totally 22 test DNA samples.Goal is to get the golbal copy number variation profile between chicken breeds.
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Project description:miRNA Transcriptome of Tibetan chicken and Pengxian yellow chicken
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Project description:Adaptation to hypoxia is a complicated and important physiological course for organisms, but the genetic mechanism underlying the adaptation is not fully understood yet. Tibetan Chicken (T), an indigenous chicken breed in China which inhabit in high areas with an altitude above 2,900 meters. Shouguang Chicken(S) and Dwarf Recessive White Chicken (DRW), two lowland chicken breeds, were used as control groups. The heart was the first functional organ to develop during the embryonic development. Furthermore, the heart is an efficient energy converter utilizing the most appropriate fuel for a given environment. Therefore, GeneChip® Chicken Genome Array was employed to identify the differentially expressed genes in embryonic hearts of Tibetan Chicken and two lowland chicken breeds in both hypoxic and normoxic incubating environments with a genome wide profile. Keywords: stress response
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Project description:Examination of whole genome DNA methylation status of two chicken breeds
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Project description:We report the genome-wide DNA methylation mapping of chicken by methylated DNA immunoprecipitation following by highthroughput sequencing, and the gene expression profile of chicken by RNA-seq. For meDIP-seq, about 17,202,074 to 27,501,760 reads were generated for the tissue and liver tissues of the red jungle fowl and the avian broiler each. We found that compared with the red jungle fowl, DNA methylation in muscle tissue of the avian broiler, showed dramatically decline on a genome-wide scale. Furthermore, the length of the highly methylated regions (HMRs) has become shorter in the avian broiler, which has suffered intense artificial selection. In addition to the global changes in DNA methylation, transcriptome-wide analysis of the two breeds of chicken revealed that the patterns of gene expression in the domestic chicken have undergone a specific bias towards a pattern that is more suited to human-made environments with variable expression in certain gene functions, such as immune response and fatty acid metabolism. Our results demonstrated a potential role of epigenetic modification in animal domestication besides the genetic variations. Examination of whole genome DNA methylation status in liver and muscle of two chicken breeds.
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Project description:Genome-wide Assessment of DNA Methylation in Chicken Cardiac Tissue Exposed to Different Incubation Temperatures and CO2 Levels
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