Sus scrofa
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA305992 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR3066483_1.fastq.gz | Fastqsanger.gz | |||
| SRR3066483_2.fastq.gz | Fastqsanger.gz | |||
| SRR3066484_1.fastq.gz | Fastqsanger.gz | |||
| SRR3066484_2.fastq.gz | Fastqsanger.gz |
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Project description:The chain of events leading from oxidation stress is still barely understood. With the emergence of high-throughput sequencing, it is now possible to discover many different biological components simultaneously. Using RNA-seq technology, we sequenced the complete transcriptome of hippocampus of Rongchang piglets exposed to iron dextran (FeDex) treatment, a potent inducer of oxidation stress. Total RNAs from hippocampus of Rongchang piglet were sequenced and 11.5 Gb sequencing data was obtained. This analysis revealed regulatory molecules involved in oxidation stress through the identification of 362 differentially expressed genes (DEGs) and the functional analysis of DEGs. Furthermore, 76 neuropeptide gene transcripts, 60 neuropeptide receptor gene transcripts, were identified in hippocampus of Rongchang piglets, even though mRNA levels of only six neuropeptide genes were significantly changed. Totally, by using the RNA-seq we elucidated for the first time the transcriptomic changes directly caused by the injection of iron dextran. This system enabled the characterization of the transcriptional response triggered by oxidation stress in hippocampus of Rongchang piglet.
2018-12-15 | GSE76007 | GEO
Project description:Weaning is a very critical period for piglets, typically accompanied by lower feed intake, weight loss after weaning and increased mortality. At weaning, piglets are exposed to many stressors, such as loss of mothering, mixing with other litters, end of lactational immunity, and a change in their environment and gut microbiota. After weaning, morphological and histological changes occur in the small intestine of piglets producing a rapid change of feeding regime which is critical for the immature digestive system. Sixteen female piglets were weaned to assess the effect of sorbic acid supplementation on the small intestine tissue transcriptome. At weaning day (T0), 4 piglets were sacrified and tissue samples collected. The remaining 12 piglets were weighted and randomly assigned to different post weaning (T5) diets. Diet A (n=6) contained 5 g/kg of sorbic acid. Diet B (n=6) is the same as Standard diet. Total RNA was isolated from ileum samples to be analyzed using the a CombiMatrix CustomArrayTM 90K platform . Even though diet had no detectable effect during the first 5 days after weaning, outcomes from this study highlighted some of the response mechanisms to the stress of weaning occurring in the piglet gut. A total of 205 differentially expressed genes were used for functional analysis using bioinformatics through BLAST2GO, Ingenuity Pathway Analysis 8.0, and the Dynamic Impact Aproach (DIA). Bioinformatics analysis revealed that Apoptosis, RIG-I-like and NOD-like receptor signaling were altered as a result of weaning. Results suggest that immune and inflammatory responses were activated and likely are a cause of small intestine atrophy as revealed by a decrease in villus height and villus/crypt ratio. Keywords: weaning, gut, gene expression, sorbic acid, microarray analysis
2014-11-14 | GSE50150 | GEO
Project description:Large White and Meishan pigs were either non-treated or injected with mammalian 1-24 ACTH (Immediate Synachten, Novartis France) at the dose of 250 µg per animal. Pigs were sacrificed either immediately after capture from their home cage (non-treated animals) or 1 hour following ACTH injection. Adrenal glands were immediately collected from pigs and frozen on dry ice and then stored at -80°C until RNA isolation. Keywords: stress response, adrenal, gene expression, pig
2008-01-07 | GSE8377 | GEO
Project description:BACKGROUND:In animal breeding, identification of causative genetic variants is of major importance and high economical value. Usually, the number of candidate variants exceeds the number of variants that can be validated. One way of prioritizing probable candidates is by evaluating their potential to have a deleterious effect, e.g. by predicting their consequence. Due to experimental difficulties to evaluate variants that do not cause an amino-acid substitution, other prioritization methods are needed. For human genomes, the prediction of deleterious genomic variants has taken a step forward with the introduction of the combined annotation dependent depletion (CADD) method. In theory, this approach can be applied to any species. Here, we present pCADD (p for pig), a model to score single nucleotide variants (SNVs) in pig genomes. RESULTS:To evaluate whether pCADD captures sites with biological meaning, we used transcripts from miRNAs and introns, sequences from genes that are specific for a particular tissue, and the different sites of codons, to test how well pCADD scores differentiate between functional and non-functional elements. Furthermore, we conducted an assessment of examples of non-coding and coding SNVs, which are causal for changes in phenotypes. Our results show that pCADD scores discriminate between functional and non-functional sequences and prioritize functional SNVs, and that pCADD is able to score the different positions in a codon relative to their redundancy. Taken together, these results indicate that based on pCADD scores, regions with biological relevance can be identified and distinguished according to their rate of adaptation. CONCLUSIONS:We present the ability of pCADD to prioritize SNVs in the pig genome with respect to their putative deleteriousness, in accordance to the biological significance of the region in which they are located. We created scores for all possible SNVs, coding and non-coding, for all autosomes and the X chromosome of the pig reference sequence Sscrofa11.1, proposing a toolbox to prioritize variants and evaluate sequences to highlight new sites of interest to explain biological functions that are relevant to animal breeding.
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Project description:Large White and Meishan pigs were either non-treated or injected with mammalian 1-24 ACTH (Immediate Synachten, Novartis France) at the dose of 250 µg per animal. Pigs were sacrificed either immediately after capture from their home cage (non-treated animals) or 1 hour following ACTH injection. Adrenal glands were immediately collected from pigs and frozen on dry ice and then stored at -80°C until RNA isolation. Keywords: stress response, adrenal, gene expression, pig 47 samples
2010-06-29 | E-GEOD-8377 | biostudies-arrayexpress
Project description:Fecal samples (N = 10) from 6- to 8-week-old wild boar piglets (Sus scrofa), collected from an animal park in Hungary in April 2011, were analyzed using viral metagenomics and complete genome sequencing. Kobuvirus (genus Kobuvirus, family Picornaviridae) was detected in all (100 %) specimens, with the closest nucleotide (89 %) and amino acid (94 %) sequence identity of the strain wild boar/WB1-HUN/2011/HUN (JX177612) to the prototype porcine kobuvirus S-1-HUN (EU787450). This study suggests that genetically highly similar (practically the same geno-/serotype) porcine kobuvirus circulate in wild boars, the wildlife counterparts of domestic pigs. Wild boars could be an important host and reservoir for kobuvirus.
| S-EPMC3541462 | biostudies-literature
Project description:RNA polyadenylation is an important step in the messenger RNA (mRNA) maturation process, and the first step is recognizing the polyadenylation signal (PAS). The PAS type and distribution is a key determinant of post-transcriptional mRNA modification and gene expression. However, little is known about PAS usage and alternative polyadenylation (APA) regulation in livestock species. Recently, sequencing technology has enabled the generation of a large amount of sequencing data revealing variation in poly(A) signals and APA regulation in Sus scrofa. We identified 62,491 polyadenylation signals in Sus scrofa using expressed sequence tag (EST) sequences combined with RNA-seq analysis. The composition and usage frequency of polyadenylation signal in Sus scrofa is similar with that of human and mouse. The most highly conserved polyadenylation signals are AAUAAA and AUUAAA, used for over 63.35% of genes. In addition, we also analyzed the U/GU-rich downstream sequence (DSE) element, located downstream of the cleavage site. Our results indicate that APA regulation was widely occurred in Sus scrofa, as in other organisms. Our result was useful for the accurate annotation of RNA 3' ends in Sus scrofa and the analysis of polyadenylation signal usage in Sus scrofa would give the new insights into the mechanisms of transcriptional regulation.
| S-EPMC8773104 | biostudies-literature
Project description:Contrary to spontaneous yawning-an ancient phenomenon common to vertebrates-contagious yawning (elicited by others' yawns) has been found only in highly social species and may reflect an emotional inter-individual connection. We investigated yawn contagion in the domestic pig, Sus scrofa. Owing to the complex socio-emotional and cognitive abilities of Sus scrofa, we posited that yawn contagion could be present in this species (Prediction 1) and influenced by individual/social factors (Prediction 2). In June-November 2018, on 104 semi-free ranging adolescent/adult pigs, 224 videos were recorded for video analysis on yawning. Kinship information was refined via genetic analyses. Statistical elaboration was conducted via GLMMs and non-parametric/randomization/cross-tabulation tests. We found yawn contagion in Sus scrofa, as it was more likely that pigs yawned when perceiving rather than not perceiving (yawning/control condition) others' yawns (response peak in the first out of three minutes). Yawn contagion was more likely: (1) in response to males' yawns; (2) as the age increased; (3) within short distance (1 m); (4) between full siblings, with no significant association between kinship and distance. The influence of kinship suggests that-as also hypothesized for Homo sapiens-yawn contagion might be linked with emotional communication and possibly contagion.
| S-EPMC7817675 | biostudies-literature
Project description:Regulatory Mechanisms of Atrial Remodeling of Mitral Regurgitation Pigs
2015-02-01 | GSE43072 | GEO