Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: On-farm broiler chicken litter monitoring

PROVIDER: PRJNA1134661 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR29842200_subreads.fastq.gz	Fastqsanger.gz
	SRR29842201_1.fastq.gz	Fastqsanger.gz
	SRR29842202_subreads.fastq.gz	Fastqsanger.gz
	SRR29842203_1.fastq.gz	Fastqsanger.gz
	SRR29842204_subreads.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 23

Similar Datasets

Proteomics investigation reveals breed specific responses to environmental enrichment and broiler meat quality

Project description:This study, conducted as part of the mEATquality European Union project, used a large intervention experiment to examine the main effects and interactions of extensification factors in higher-welfare, non-organic systems with relatively low chicken stocking density. The study focused on how chicken genetics and on-farm enrichments (as two extensification factors) influence broiler performance, intrinsic meat quality and the molecular mechanisms underlying these traits with the aim of supporting improved production strategies.

2026-05-29 | PXD066390 | Pride

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.

2010-06-11 | GSE19469 | GEO

Effect of an immune challenge and feed supplements on broiler chicken individual breast muscle protein synthesis

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

Fold change of expression in Aseel (an indigenous chicken breed) as compared to broiler chicken in 7th day of embryonic stage

Project description:The expression of genes were analysed in 7th day of embryonic stage between Aseel, an indigenous slow-growing chicken, and control broiler, a fast-growing broiler chicken line. The whole embryo was collected in TRIZOL and total RNA was isolated. The expression profile of gene was determined in 64k Agilent chicken microarray chip. The Cy3 dye was used for detection. The fold change of expression was analysed in Aseel as compared to broiler chicken line.

2014-10-17 | GSE62443 | GEO

Fold change of expression in Aseel (an indigenous chicken breed) as compared to broiler chicken in muscle of 18th day of embryonic stage

Project description:The expression of genes were analysed in muscle of 18th day of embryonic stage between Aseel, an indigenous slow-growing chicken, and control broiler, a fast-growing broiler chicken line. The whole embryo was collected in TRIZOL and total RNA was isolated. The expression profile of gene was determined in 64k Agilent chicken microarray chip. The Cy3 dye was used for detection. The fold change of expression was analysed in Aseel as compared to broiler chicken line.

2014-10-17 | GSE62444 | GEO

chicken gut metagenome

Project description:Broiler chicken gut/litter Targeted Locus (Loci)

| PRJNA246596 | ENA

Examination of whole genome DNA methylation status of two chicken breeds

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

Dehong chicken blood samples: Control vs. 6 chicken blood samples belonging to 3 different breeds

Project description:Copy number variation profiles comparing control female Dehong chicken blood DNA with 3 different chicken breeds (white Leghorn, Cobb broiler, and Dou chicken) blood DNA. Each test breed had one male and one female sample, for a total of 6 test DNA samples. The goal is to determine the global copy number variation profiles between chicken breeds.

2011-04-12 | GSE28526 | GEO

Metagenomes

Project description:Broiler Chicken Cloacal and Litter Meta-genomic Samples

| PRJNA598014 | ENA

Single-cell RNA sequencing of the spleen reveals differences in the mechanisms of resistance to bacterial infection between different chicken breeds

Project description:Bacterial infections remain an important cause of morbidity in poultry production. The molecular characteristics and dynamic changes in immune cell populations after bacterial infection have yet to be fully understood. Beijing-You chicken and Cobb broiler, two broiler breeds with different disease resistance, were infected with Salmonella typhimurium, and inflammation models were constructed. We characterized chicken spleen CD45+ immune cells by single-cell RNA sequencing.

2023-10-01 | GSE242458 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data