Boar RRBS
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB35306 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:In this study, differentially expressed (DE)piRNAs of fresh and frozen-thawed sperm with different freeze tolerance compacity from giant panda and boar were evaluated. The results showed 1160 (22 down-regulated and 1138 up-regulated) and 384 (110 up-regulated and 274 down-regulated) differentially expressed (DE) piRNAs were identified in giant panda and boar sperm, respectively. Gene ontology (GO) enrichment analysis revealed that the target DE mRNAs of DE piRNAs were mainly enriched in biological regulation, cellular process and metabolic process in giant panda and boar sperm. Moreover, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that the target DE mRNAs of DE piRNAs were only distributed on DNA replication and cAMP signaling pathway in giant panda, but cAMP, cGMP and MAPK signaling pathway in boar sperm which were considered as part of olfactory transduction pathway.Conclusion:Olfactory transduction related pathways maybe contributed to different freeze tolerance compacity between giant panda and boar sperm, which will benefit to further understand the molecular mechanism of sperm cryoinjury and freezability.
2021-04-19 | GSE163128 | GEO
Project description:In present study, we first tried to reveal the transcriptome-wide m6A methylation pattern in boar fresh sperm (Fs) and frozen-thawed sperm (Fts) through MeRIP-seq, which demonstrates occurrence the diverse m6A modification patterns during cryopreservation. Results: the expression of m6A modification enzymes were significantly dysregulated in sperm during cryopreservation. Furthermore, the m6A peaks were mainly enriched in coding regions and near stop codons with classical RRACH motifs. In Fts, a total of 1754 differentially methylated m6A genes containing 1928 differentially methylated peaks were identified as compared to Fs. Bioinformatics analysis revealed the role of these genes containing significantly altered m6A peaks (DMMGs) were significantly enriched in terms of metabolism and transcription, as well as a number of DMMGs were annotated to ubiquitin mediated proteolysis, AMPK, mTOR and MAPK signaling pathways. Furthermore, the joint analysis of DMMGs and differentially expressed genes indicated that both of these play a vital role in sperm energy metabolism and apoptosis. Conclusion: Our study is first to reveal the dynamic m6A modification in mRNAs of boar sperm during cryopreservation, and provides a new evidence regarding the potential roles of m6A in modulating sperm motility, apoptosis and metabolism. Keywords: N6-methyladenosine (m6A); Boar sperm; Cryopreservation; MeRIP-seq
2021-06-09 | GSE164691 | GEO
Project description:Chromatin packaging in sperm protects it against DNA fragmentation, and the importance of proper chromatin packaging for boar fertility outcome has become increasingly evident. Little is known however about the molecular mechanisms underlying differences in sperm DNA fragmentation and an understanding of the genes controlling this sperm parameter could help in selecting the best boars for AI use. The aim of this study was to identify differentially expressed genes in testis of Norsvin Landrace and Duroc boars with good and bad sperm DNA fragmentation using transcriptome sequencing and to use the data for polymorphism search. RNA sequence reads were obtained using Illumina technology and mapped by TopHat using the Ensembl pig database. Differentially expressed genes and pathways were analyzed using the R Bioconductor packages edgeR and goseq respectively. Using a false discovery rate of 0.05, 309 and 375 genes were found displaying significant differences in expression level between the good and bad condition in Landrace and Duroc respectively. Of the differentially expressed genes, 72 were found in common for the two breeds. Gene ontology analysis revealed that terms common for the two breeds included extracellular matrix, extracellular region and calcium ion binding. Additionally, different metabolic processes were enriched in Landrace and Duroc, whereas immune response ontologies were found to be important in Landrace. SNP detection in Landrace/Duroc identified 53182/53931 variants in 10924/10748 transcripts and of these, 1573/1827 SNPs occurred in 189/241 unique genes that were also differentially expressed. Possible high impact variants were detected using SnpEff. Transcriptome sequencing identified differentially expressed genes and nucleotide variants related to differences in sperm DNA fragmentation, and functional annotation of the genes pointed towards important biochemical pathways. This study provides insights into the genetic network underlying this trait and is a first step towards using sperm DNA fragmentation for predicting boar fertility.
2017-09-01 | GSE74934 | GEO
Project description:DIA of boar sperm with different treatment and PRM validation
2021-09-06 | PXD028213 | iProX
Project description:The perinuclear theca (PT) is a highly condensed, largely insoluble protein structure that surrounds the nucleus of eutherian spermatozoa. While this structure is known to be important for fertilization, little is known regarding its proteomic composition. Recent reports have indicated that the PT unexpectedly houses several somatic proteins, such as core histones, which may be important post-fertilization during re-modelling of the male pronucleus. To explore the proteomic composition of the PT we performed the first in depth, label-free proteomic characterization of the PT of boar spermatozoa. To do this, a unique subcellular fractionation protocol was first performed to isolate the PT and increase our ability to detect lowly abundant sperm proteins. Through the use of this subcellular fractionation technique we were able to quantify 1802 proteins, a result that represents unparalleled depth of coverage for the boar sperm proteome and exceeds the entire known proteome of the Sus scrofa species so far. In the PT structure itself we identified 813 proteins and confirmed the presence of previously characterized PT proteins including the core histones H2A, H2B, H3 and H4, as well as Ras-related protein Rab-2A (RAB2A) and Rab-2B (RAB2B) amongst other RAB proteins. In addition to these previously characterized PT proteins, our data also revealed that the PT is replete in proteins critical for sperm-egg fusion including: Izumo sperm-egg fusion proteins 1-4 (IZUMO1-4) and phosphoinositide phospholipase C (PLCZ1).
2022-03-09 | PXD030020 | Pride
Project description:All-genome genotyping data from French wild boar populations could be useful for diversity studies in the wild boar species as well as for phylogeny studies with domestic pig populations. The data produced in this experiment concern 362 wild boars collected between 2013 and 2019 in various French departments. The biological samples that were collected were either blood samples or ear biopsies. Genomic DNA was extracted from cells after proteinase K lysis and ethanol precipitation. DNA was hybridized on the GeneSeek Genomic Profiler porcine beadchip (GGP70K HD Porcine Illumina) using Infinium technology. Fluorescence intensity data obtained for each Single Nucleotide Polymorphism were analyzed with GenomeStudio software to infer genotypes. In addition, the raw fluorescence data could be useful for Copy Number Variation studies.
2022-01-25 | E-MTAB-10591 | biostudies-arrayexpress
Project description:Brucella suis infects macrophages and dendritic cells. Wild boars act as reservoirs and carriers of Brucella suis biovar 2, and there is evidence that wild boar can be the main source of infection for domestic pigs through the venereal route. Transmission through this route could be an important path for disesease dissemination. The result from this study will contribute to the overall understanding of the molecular pathogenic mechanisms involved during Brucella suis infection in European wild boar. Experiment Overall Design: In this study we preliminarily characterized differential gene expression in European wild boar naturally infected with Brucella suis biovar 2 using Microarray hybridization and Real Time RT-PCR analysis. Since Brucella suis acts by infecting macrophages, we used spleen cells to analyze the gene expression response to Brucella suis infection.
2009-10-02 | E-GEOD-17492 | biostudies-arrayexpress
Project description:Sperm cells are characterized by a unique epigenome, and an incorrect establishment of DNA methylation patterns during the differentiation of male germ cells into spermatozoa has been associated with male infertility in several species. While bull semen is widely used in artificial insemination, the literature describing DNA methylation in bovine sperm is still scarce. The purpose of this study is to compare the methylomes of sperm and somatic cell types in cattle using the RRBS technology.
2018-05-03 | GSE102169 | GEO
Project description:Identification of MicroRNAs Expressed in Porcine Sperm Cells. Commerical boar sperm samples were used.
2008-12-01 | E-MEXP-1788 | biostudies-arrayexpress