RM424Trio
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB12092 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR1189150.fastq.gz | Fastqsanger.gz | |||
| ERR1189150_1.fastq.gz | Fastqsanger.gz | |||
| ERR1189150_2.fastq.gz | Fastqsanger.gz | |||
| ERR1189151_1.fastq.gz | Fastqsanger.gz | |||
| ERR1189151_2.fastq.gz | Fastqsanger.gz |
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Project description:Rapid Discovery of De Novo Deleterious Mutations in Cattle Using Genome Sequence Data: Enhancing the Value of Farm Animals as Model Species
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Project description:Rapid Discovery of De Novo Deleterious Mutations in Cattle Using Genome Sequence Data: Enhancing the Value of Farm Animals as Model Species
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Project description:In this study, samples of 16 dairy cows from a MAP infected farm were used. Serum, milk and fecal samples were collected. Categorizing these cows into two groups based on their MAP infection status different standard methods for detection MAP were applied. Healthy controls showed no positive results in enzyme-linked immunosorbent assay (ELISA) with serum and milk samples (cattletype MAP Ab, Qiagen, Hilden, Germany; In-direct, IDVet, Grabels, France) and after cultivation of fecal samples on commercial Her-rold´s Egg Yolk Agars (HEYM agar, Becton Dickinson, Heidelberg, Germany) for 12 weeks. Cows with positive results were grouped into MAP infected cows. Specifically, for mass spectrometry analysis serum of seven MAP infected cows and seven healthy controls were used. All animals were from the same farm and were kept under the same environmental conditions. For additional mass spectrometry analysis with a further control group sam-ples of 21 dairy cows from an uninfected farm were examined. All cattle from this farm showed negative results in ELISA with serum and milk samples. Additionally, there was never a positive result in regularly tested fecal samples and sock swab samples of this farm. For verification of differential CTSS expression in Western blot analysis five dairy cows from another infected farm were consultedincluded. MAP status of these cows was analyzed by cultivation of fecal samples on HEYM agar for 12 weeks and ELISA with se-rum samples. In detail, two cattle were categorized into healthy controls and three cattle into MAP infected cows. Withdrawal of bovine venous whole blood and experi-mental protocols were approved by the local authority, Government of Upper Bavaria, permit no. ROB-55.2-2532.Vet_03-17-106.
2024-06-22 | PXD048042 | Pride
Project description:The importance of the adrenal gland in regard to lactation and reproduction in cattle has been recognized early. Due to consumers interest in animal welfare and the impact of stress on economically important traits in farm animals the adrenal gland and its function within the stress response is still of increasing interest. Especially the molecular mechanisms and pathways that are involved in the stress related effects on economically important traits in farm animals are not studied in full detail. Gene expression is an important mechanism underlying complex traits. Genetic variants affecting the transcript abundance are thought to affect the manifestation of an expressed phenotype. Therefore we investigated the genetic background of adrenocortical gene expression by applying an adaptive linear rank test to identify genome-wide expression quantitative trait loci (eQTL) for adrenal cortex transcripts in cattle.
2016-12-01 | GSE75371 | GEO
Project description:De Novo Mutation Discovery in Plasmodium falciparum
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Project description:Enhancing climate resilience and sustainable production for animals in harsh environments are important goals for the livestock industry given the predicted impacts of climate change. Rapid adaptation to extreme climatic conditions has already been imposed on livestock species, including those exported after Columbus’ arrival in the Americas. We compared the methylomes of two Creole cattle breeds living in tropical environments with their putative Spanish ancestors to understand the epigenetic mechanisms underlying rapid adaptation of a domestic species to a new and more physiologically challenging environment. Reduced representation bisulfite sequencing (RRBS) was used to assess differences in methylation in Creole and Spanish samples and revealed 334 differentially methylated regions (DMRs) using high stringency parameters (p-value < 0.01, 4 CpGs within a distance of 200 bp, mean methylation difference > 25%), annotated to 263 unique features. Gene ontology analysis revealed candidates involved in tropical adaptation processes, including genes differentially hyper- or hypomethylated above 80% in Creole samples displaying biological functions related to immune response (IRF6, PRGDR, FAM19A5, PRLYRP1), nervous system (GBX2, NKX2-8, RPGR), energy management (BTD), heat resistance (CYB561) and skin and coat attributes (LGR6). Our results entail that major environmental changes imposed on Creole cattle has had an impact on their methylomes measurable today, which affects genes implicated in important pathways for adaptation. Although further work is needed, this first characterization of methylation patterns driven by profound environmental change provides a valuable pointer for the identification of biomarkers of resilience for improved cattle performance and welfare under predicted climatic change models.
2019-07-01 | GSE101796 | GEO
Project description:Background The goat (Capra hircus) represents one of the most important farm animal species. It is reared in all continents with an estimated world population of about 800 million of animals. Despite its importance, studies on the goat genome are still in their infancy compared to those in other farm animal species. Comparative mapping between cattle and goat showed only a few rearrangements in agreement with the similarity of chromosome banding. We carried out a cross species cattle-goat array comparative genome hybridization (aCGH) experiment in order to identify copy number variations (CNVs) in the goat genome analysing animals of different breeds (Saanen, Camosciata delle Alpi, Girgentana, and Murciano-Granadina) using a tiling oligonucleotide array with ~385,000 probes designed on the bovine genome. Results We identified a total of 161 CNVs (an average of 17.9 CNVs per goat), with the largest number in the Saanen breed and the lowest in the Camosciata delle Alpi goat. By aggregating overlapping CNVs identified in different animals we determined CNV regions (CNVRs): on the whole, we identified 127 CNVRs covering about 11.47 Mb of the virtual goat genome referred to the bovine genome (0.435% of the latter genome). These 127 CNVRs included 86 loss and 41 gain and ranged from about 24 kb to about 1.07 Mb with a mean and median equal to 90,292 bp and 49,530 bp, respectively. To evaluate whether the identified goat CNVRs overlap with those reported in the cattle genome, we compared our results with those obtained in four independent cattle experiments. Overlapping between goat and cattle CNVRs was highly significant (P<0.0001) suggesting that several chromosome regions might contain recurrent interspecies CNVRs. Genes with environmental functions were over-represented in goat CNVRs as reported in other mammals. Conclusions We describe a first map of goat CNVRs. This provides information on a comparative basis with the cattle genome by identifying putative recurrent interspecies CNVs between these two ruminant species. Several goat CNVs affect genes with important biological functions. Further studies are needed to evaluate the functional relevance of these CNVs and their effects on behavior, production, and disease resistance traits in goats.
2010-11-09 | GSE24436 | GEO
Project description:The objective was to study the transcriptomic changes in adipose tissue in the early stages of lactation, specifically in Bos Taurus, Holstein dairy cattle as a function of milk production and genetic merit. Chip quality backgrounds averaged below 50 units, and 3'/5' bias on control genes < 2.0. Correlations among replicates were > 0.85. The design was a simple paired sampling, with time (30 d prepartum and 14 d postpartum as the sampling times. There was no dietary manipulation. Animals were all first calving Holstein heifers, all raised on the same farm on the same diet
2010-05-27 | E-GEOD-21535 | biostudies-arrayexpress
Project description:Background: Farm exposures in early life reduce the risks for childhood allergic diseases and asthma. There is less information about how farm exposures relate to respiratory illnesses and mucosal immune development. Objective: We hypothesized that children raised in farm environments have a lower incidence of viral illnesses over the first two years of life than non-farm children. We also analyzed between farm exposures or respiratory illnesses were related to patterns of nasal cell gene expression. Methods: The Wisconsin Infant Study Cohort (WISC) birth cohort enrolled farm and non-farm pregnant women from central Wisconsin. Parents reported prenatal farm and other environmental exposures. Illness frequency and severity were assessed using illness diaries and periodic surveys. Nasopharyngeal cell gene expression at age two years was compared to farm exposure and respiratory illness history. Results: There was a higher rate of respiratory illnesses in the non-farm vs. farm group (rate ratio 0.82 [0.69,0.97], p=0.020), but no significant differences in wheezing illnesses. There was a stepwise reduction in rates of respiratory illnesses in children exposed at least weekly to 0, 1, or ≥2 animals (p=0.006). In analyzing nasal cell gene expression, farm exposures and preceding respiratory illnesses were positively related to gene signatures for mononuclear cells and innate and antimicrobial responses. Conclusions: Children exposed to farms and farm animals had lower rates of respiratory illnesses over the first two years of life. Both farm exposures and preceding respiratory illnesses were associated with increased innate immune responses, suggesting that these exposures stimulate mucosal immune responses to reduce subsequent illness frequency.
2024-01-29 | GSE233761 | GEO
Project description:To assess how different levels of stress exposure affect gene regulation mechanisms in cattle, we investigated gene expression in 13 Italian Red Pied dairy cows falling in the high- and low-variant tails of the distribution of milk cortisol concentration (MC), a neuroendocrine biomarker of stress in dairy cows, measured in 126 animals belonging to the same farm in the framework of the Gen2Phen Italian project. The ‘low-’ and ‘high-cortisol’ groups of animals had MC<370 pg/ml and>810 pg/ml, respectively. To date, 13 animals (6 low- and 7 high-MC) have been sequenced. We detected significant fold differences in the expression of 324 genes. KEGG and Gene Ontology (GO) pathway analyses indicated that these genes were mainly involved in immune regulatory pathways, glucocorticoids metabolism and nervous system functions.
2020-09-30 | GSE146971 | GEO