Biomarkers of stressed chickens across different biomes
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB34868 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR3630380.fastq.gz | Fastqsanger.gz | |||
| ERR3630380_1.fastq.gz | Fastqsanger.gz | |||
| ERR3630380_2.fastq.gz | Fastqsanger.gz | |||
| ERR3630390.fastq.gz | Fastqsanger.gz | |||
| ERR3630390_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 219 |
Similar Datasets
Project description:Here, we applied a microarray-based metagenomics technology termed GeoChip 5.0 to examined functional gene structure of microbes in three biomes, including boreal, temperate and tropical area.
2024-05-10 | GSE172195 | GEO
Project description:Transcriptional profiling of the jejunum mucosa with 1.5 fold-change reporter genes in comparing control black-boned chickens under normal temperature (NT) conditon with heat-stress treated black-boned chickens under high temperature (HT) condition. Goal was to determine the differentially expressed genes (DEGs) in co-family black-boned chickens exposure to heat stress based on global chicken gene expression.
2015-07-28 | GSE71352 | GEO
Project description:Herein, we evaluated the changes in biological functions in soils across global biomes through the identification and quantification of proteins. This knowledge is essential to provide one stepforward in soil microbial ecology in order to decipher the cellular and molecular mechanisms employed by soil microbial communities to adapt to their environment and to explain the potential responses of microbial communities, and their microbially-driven ecosystem services, to global change and land use. Our study aims to provide the most comprehensive assessment on the structure and function of the topsoil metaproteome across global biomes, and hence provide direct identification of the most domimant protein-encoded functions in terrestrial ecosystems.
2023-02-24 | PXD018448 | Pride
Project description:Transcriptional profiling of the jejunum mucosa with 1.5 fold-change reporter genes in comparing control black-boned chickens under normal temperature (NT) conditon with heat-stress treated black-boned chickens under high temperature (HT) condition. Goal was to determine the differentially expressed genes (DEGs) in co-family black-boned chickens exposure to heat stress based on global chicken gene expression. Two-condition experiment, HT vs. NT Treatment. Biological replicates: 3 control replicates, 3 heat stressed replicates.
2015-07-28 | E-GEOD-71352 | biostudies-arrayexpress
Project description:Meat type chickens have limited capacities to cope with high environmental temperatures, sometimes leading to important mortality in farms and subsequent economic loss. One of the strategies to increase the sustainability of broiler chicken production is to enhance their adaptive capacities to face heat exposure using heat conditioning (C) during embryogenesis. This strategy was shown to improve thermotolerance in later life. The aim of this study was to determine the effect of C (39.5°C, 12h/24 vs 37.8°C from d7 to d16 of embryogenesis) and of a subsequent heat challenge (32°C for 5h, CH) applied on d34, on global gene expression in the Pectoralis major muscle (PM). Chicken Genome Array (60 K) was used to compare muscle gene expression profiles of Control (T) and heat-conditioned C chickens (characterized by low body temperature) reared at 21°C, and reared at 32°C (TCH and CCH respectively) in a dye-swap design with four comparisons and 8 broilers per condition. Real-time RT-PCR was subsequently performed to validate differential expressions in each comparison. Gene ontology, clustering and network building strategies were used. This study was performed with the financial support of the French Agence Nationale de la Recherche, Project «Jeunes Chercheuses et Jeunes Chercheurs», ANR-09-JCJC-0015-01, THERMOCHICK.
2016-05-09 | GSE70756 | GEO
Project description:Production animals are constantly subjected to early adverse environmental conditions that influence the adult phenotype and produce epigenetic effects. CpG dinucleotide methylation in red blood cells (RBC) could be a useful epigenetic biomarker to identify animals subjected to chronic stress in the production environment. Here we compared a reduced fraction of the RBC methylome of chickens exposed to social isolation to non-exposed. These experiments were performed in two different locations: Brazil and Sweden. The aim was to identify stress-associated DNA methylation profiles in RBC across these populations, in spite of the variable conditions to which birds are exposed in each facility and their different lineages. Birds were increasingly exposed to a social isolation treatment, combined with food and water deprivation, at random periods of the day from weeks 1-4 after hatching. We then collected the RBC DNA from individuals and compared a reduced fraction of their methylome between the experimental groups using two bioinformatic approaches to identify differentially methylated regions (DMRs): one using fixed-size windows and another that preselected differential peaks with MACS2. Three levels of significance were used (P ≤ 0.05, P ≤ 0.005, and P ≤ 0.0005) to identify DMRs between experimental groups, which were then used for different analyses. With both of the approaches more DMRs reached the defined significance thresholds in BR individuals compared to SW. However, more DMRs had higher fold change values in SW compared to BR individuals. Interestingly, ChrZ was enriched above expectancy for the presence of DMRs. Additionally, when analyzing the locations of these DMRs in relation to the transcription starting site (TSS), we found three peaks with high DMR presence: 10 kb upstream, the TSS itself, and 20-40 kb downstream. Interestingly, these peaks had DMRs with a high presence (>50%) of specific transcription factor binding sites. Three overlapping DMRs were found between the BR and SW population using the most relaxed p-value (P ≤ 0.05). With the most stringent p-value (P ≤ 0.0005), we found 7 and 4 DMRs between treatments in the BR and SW populations, respectively. This study is the first approximation to identify epigenetic biomarkers of long-term exposure to stress in different lineages of production animals.
| S-EPMC7667380 | biostudies-literature
Project description:DNA was isolated from whole red blood cells from various lines and crosses of broiler chickens. DNA was genotyped using Axiom genome-wide chicken array and cel files were analyzed using Axiom Analysis Suite Software (version 3.0.1) with Gallus gallus 5.0 using the software's Best Practices for agricultural animals. The results were exported (Genotyping_Data-3-21-2018.vcf) for all genotype calls and text file of all SNPs with >= 97% call rate rate was also produced for filtering the VCF file (ALL_SNPSs_with_Call_Rate_97_Plus_3-21-2018).
2019-05-25 | GSE131764 | 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.
2010-06-11 | GSE19469 | GEO