Ontology highlight
ABSTRACT:
PROVIDER: PRJNA893352 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR22016500_1.fastq.gz | Fastqsanger.gz | |||
| SRR22016500_2.fastq.gz | Fastqsanger.gz | |||
| SRR22016501_1.fastq.gz | Fastqsanger.gz | |||
| SRR22016501_2.fastq.gz | Fastqsanger.gz | |||
| SRR22016421_1.fastq.gz | Fastqsanger.gz |
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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.
2010-04-02 | E-GEOD-21167 | biostudies-arrayexpress
Project description:<p><strong>INTRODUCTION:</strong> To decrease antibiotic resistance, their use as growth promoters in the agricultural sector has been largely abandoned. This may lead to decreased health due to infectious disease or microbiome changes leading to gut inflammation.</p><p><strong>OBJECTIVES:</strong> We aimed to generate a m/z signature classifying chicken health in blood, and obtain biological insights from the resulting m/z signature.</p><p><strong>METHODS:</strong> We used direct infusion mass-spectrometry to determine a machine-learned metabolomics signature that classifies chicken health from a blood sample. We then challenged the resulting models by investigating the classification capability of the signature on novel data obtained at poultry houses in previously unseen countries using a leave-one-country-out (LOCO) cross-validation strategy. Additionally, we optimised the number of mass/charge (m/z) values required to maximise the classification capability of Random Forest models, by developing a novel ranking system based on combined univariate t-test and fold-change analyses and building models based on this ranking through forward and reverse feature selection.</p><p><strong>RESULTS:</strong> The multi-country and LOCO models could classify chicken health. Both resulting 25-m/z and 3784-m/z signatures reliably classified chicken health worldwide. Through mummichog enrichment analysis on the large m/z signature, we found changes to amino acid metabolism, including branched chain amino acids and polyamines.</p><p><strong>CONCLUSION:</strong> We reliably classified chicken health from blood, independent of genetic-, farm-, feed- and country-specific confounding factors. The 25-m/z signature can be used to aid development of a per-metabolite panel. The extended 3784-m/z version can be used to gain a deeper understanding of the metabolic causes and consequences of low chicken health. Together, they may facilitate future treatment, prevention and intervention.</p>
2023-08-08 | MTBLS5065 | MetaboLights
Project description:Background Understanding the genetic basis of phenotypic diversity is a challenge in contemporary biology. Domestication provides a model for unravelling aspects of this, for example with respect to stress sensitivity. Ancestral Red Junglefowl (RJF) show more fearful behaviour and a more pronounced HPA-axis reactivity than its domesticated descendant White Leghorn (WL). By comparing adrenal global gene transcription profiles between WL and RJF as well as their plasma levels of adrenal hormones in response to an acute stress event, we aimed at investigating the molecular basis for the altered physiological stress responsiveness in domesticated chicken.
2015-10-30 | E-MTAB-3622 | biostudies-arrayexpress
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 gene expression profiles in liver and muscle tissues of two chicken breeds.
2010-04-02 | E-GEOD-21169 | biostudies-arrayexpress
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.
2010-04-02 | GSE21169 | GEO
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.
2010-04-02 | GSE21167 | GEO
Project description:Domesticated animals share a unique set of morphological and behavioural traits, jointly referred to as the domesticated phenotype. These include modified growth, reproduction, metabolism, pubertal development and stress response. Striking similarities amongst a range of unrelated domesticated species suggest that similar regulatory mechanisms may underlie the domesticated phenotype. Several previous studies have focused on the brain to find mechanisms underlying domestication effects on the stress response, whereas the potential role of the pituitary gland as a target of domestication is highly overlooked. Here, we study gene expression in the pituitary gland of the domesticated White Leghorn chicken and its ancestor, the Red Junglefowl. We exposed chicken of both breeds to 15 minutes of restraint stress. We then culled the animals and dissected out the pituitary gland and snap froze them. RNA was later extracted from the pituitaries and gene expression was measured using Agilent microarray.
2018-03-31 | E-MTAB-6269 | biostudies-arrayexpress
Project description:Transposable elements (TEs) are genomic parasites that constitute the most abundant portions of higher plant genomes. However, whether TE selection occurred during crop domestication remains unknown. HUO is active under normal growth conditions, present at low copy numbers, inserts preferentially into regions capable of transcription, but absent in almost all modern varieties, indicating its removal during rice domestication and modern rice breeding. HUO triggers genomic immunity and dramatically alters genome-wide methylation levels and small RNA biogenesis, as well as global gene expression. Its presence specifically affects agronomic traits by decreasing yield performance and disease resistance but enhancing salt tolerance, which mechanistically explains its domestication removal. Thus, our study reveals a unique retrotransposon as a negative target for maintaining genetic and epigenetic stability during crop domestication and selection.
2018-03-08 | GSE78900 | GEO
Project description:The conservation and development of chicken has considerably affected human activities, but the admixture history of chicken breeds has so far been poorly demonstrated especially for Chinese indigenous breeds. Using genotypes from 580961 single nucleotide polymorphism markers scored in 1201 animals, we evaluate the genetic diversity (heterozygosity and proportion of polymorphic markers), Linkage disequilibrium (LD) decay, population structure (principal component analysis and neighbor-joining tree), genetic differentiation (FST and genetic distance) and migration events (Treemix and f-statistics) of eight domesticated chicken breeds. All population analytical methods reveal patterns of hybridization which occurred after divergence in Tibetan chicken. We argue that chicken migration and admixture followed by trade have been important forces in shaping modern Chinese chicken genomic variation. Moreover, isolation by distance may play critical role in the shaping genomic variation within Eurasia continent chicken breeds.
2019-10-07 | GSE127968 | GEO
Project description:We characterized the SF proteome of the polyandrous Red junglefowl, Gallus gallus, the wild species that gave rise to the domestic chicken. We identify 1,141 SFPs, including proteins involved in immunity and antimicrobial defences, sperm maturation, and fertilisation, revealing a functionally complex SF proteome. This includes a predominant contribution of blood plasma proteins that is conserved with human SF. By comparing the proteome of young and old males with fast or slow sperm velocity in a balanced design, we identify proteins associated with ageing and sperm velocity, and show that old males that retain high sperm velocity have distinct proteome characteristics. SFP comparisons with domestic chickens revealed both qualitative and quantitative differences likely associated with domestication and artificial selection. Collectively, these results shed light onto the functional complexity of avian SF, and provide a platform for molecular studies of fertility, reproductive ageing, and domestication.
2016-12-23 | PXD005160 | Pride