Sus scrofa
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA309086 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR3105510.fastq.gz | Fastqsanger.gz | |||
| SRR3105507.fastq.gz | Fastqsanger.gz | |||
| SRR3105508.fastq.gz | Fastqsanger.gz | |||
| SRR3105509.fastq.gz | Fastqsanger.gz |
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Project description:Oxidative stress is involved in the human diseases and developmental retardation of animals. The molecular mechanisms that mediate the response of neuron to oxidative stress have been extensively studied. MicroRNAs (MiRNAs) are a type of small non-coding RNAs that regulate nearly all aspects of nerve development and survival, including apoptosis. However, the effect of oxidative stress on the expression of miRNAs of hippocampus of Rongchang piglets, which are regarded as the good production animal and biomedical model has not been investigated. In this study, oxidative stress was induced in newborn piglets by means of intra-muscular injection of iron. Injection of iron significantly increased several markers of oxidative stress in serum of Rongchang piglets. RNA-sequencing (RNA-seq) technology and bioinformatics were used to uncover the differently expressed miRNAs and target genes induced by oxidative stress in the ventral hippocampus (VH) and dorsal hippocampus (DH) of Rongchang piglets, respectively. Results revealed 2790 conserved miRNAs belonging to 279 miRNA families, 326 known miRNAs and 702 novel miRNAs. The sub-tissue specificity was displayed with 54 differentially expressed miRNAs being found between VH and DH. At the same time, the injection of iron induced 59 and 46 differentially expressed miRNAs in VH and DH, respectively. The analysis of target genes showed that 6 known miRNAs (ssc-miR-183, ssc-miR-383, ssc-miR-193a-5p, ssc-miR-182, ssc-miR-7138-5p and ssc-miR-1271) commonly targeted to ADM2. In addition, GO and KEGG pathway analysis showed that these differentially expressed miRNAs induced by the injection of iron were involved in the pathways that regulate the expression of genes associated with oxidative stress. Our study provided an overview of miRNAs expression profile of functional sub-region of hippocampus in Rongchang piglets and shed light into the significantly changed miRNAs after the injection of iron, which will lead to further understanding of the important roles of miRNAs in hippocampus of Rongchang piglets during the process of oxidative stress.
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Project description:The effect of iron dextran on the transcriptome of hippocampus in Rongchang piglet
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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: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
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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:Map the causative gene of hearing loss in Chinese Rongchang pigs by GWAS
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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:Gene expression of characteristic chondrogenic markers and miRNA expression were analyzed in cells cultured in differentiation medium and significant differences were found between gelation/PRP microgels and those containing only pure gelatin. We used microarrays to detail the miRNA expression in studied cell cultures for identification the expression of miRNA and study the up- and down-regulated miRNA associated.
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