DNA methylome of tea tree
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ABSTRACT:
PROVIDER: PRJNA491190 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Bisulfite treatment libraries were made to characterize the DNA methylome of tea tree
2018-09-15 | GSE119992 | GEO
Project description:RNA sequencing (RNA-Seq) was used in our study to elucidate the mechanism of Tea tree oil (TTO) as a potential antibacterial agent to evaluate differentially expressed genes and functional network analysis in S. aureus ATCC 29213 biofilms.
2016-08-19 | GSE85787 | GEO
Project description:RNA sequencing (RNA-Seq) was used in our study to elucidate the mechanism of Tea tree oil (TTO) as a potential antibacterial agent to evaluate differentially expressed genes and functional network analysis in S. aureus ATCC 29213 biofilms. Staphylococcus aureus biofilm cells were exposed for 60 minutes to TTO at concentration of 1/2ÃMBIC (1 mg/ml).2 samples including 2 control samples are analyzed.
2016-08-19 | E-GEOD-85787 | biostudies-arrayexpress
Project description:Purpose: High-throughput RNA sequencing has been used to examine mRNA expression profiles in fungal cells treated with essential oils. The goals of this study are to analyze the global gene expression profiles in Botrytis cinerea with or without tea tree oil and its two characteristic components treatment by RNA-Seq. Methods: The mRNA profiles of Botrytis cinerea with or without tea tree oil and its two characteristic components treatment were generated by deep sequencing, in triplicate, using Illumina HiSeq™ 2500 sequencing platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR was performed to verified the sensitivity of the RNA-seq method. Results: After high-throughput RNA sequencing, reads were filtered to yield 111.22 Gb of clean sequence data. The GC content for all samples exceeded 45%. The Q20 ratio (used to evaluate reads quality) was greater than 94%, and Q30 base percentage was at least 87.07%. Altered expression of 7 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Most differentially expressed genes (DEGs) from B. cinera cells treated with terpinen-4-ol participated in biosynthesis of secondary metabolites, and the metabolism of amino acid, carbohydrate and lipid. 1,8-cineole mainly affected DEGs involved in genetic information processing, and thus inducing cell death. Conclusions: Terpinen-4-ol exerts antifungal activity mainly by blocking the expression of genes related to cell integrity and mitochondrial function. 1,8-cineole primarily affects genes involved in genetic information processing including DNA replication, transcription and repair. This study provides insight into the molecular mechanism by which tea tree oil acts against Botrytis cinerea based on the data from RNA-seq.
2019-10-03 | GSE138291 | GEO
Project description:Tea (Camellia sinensis (L.) O. Kuntze) is an important non-alcoholic commercial beverage crop. Tea tree is a perennial plant, and winter dormancy is its part of biological adaptation to environmental changes. We recently discovered a novel tea tree cultivar that can generate tender shoots in winter, but the regulatory mechanism of this ever-growing tender shoot development in winter is not clear. In this study, we conducted a proteomic analysis for identification of key genes and proteins differentially expressed between the winter and spring tender shoots, to explore the putative regulatory mechanisms and physiological basis of its ever-growing character during winter.
2022-02-23 | PXD008958 | Pride
Project description:Effects of 0 and 100mg/kg tea tree oil supplementation on hepatopancreas proteomics of macrobrachium rosenbergii
2022-05-19 | PXD032896 | iProX
Project description:DNA methylation is critical for development and is strongly associated with gene regulation. Variation in the DNA methylome between closely related species may reveal unique functional adaptation. We have implemented a novel inter-primate DNA methylation genome-wide analysis between human, chimpanzee and rhesus macaque to identify human species-specific Differentially Methylated Regions (human s-DMRs) in orthologous loci. We analysed the peripheral blood cell DNA methylomes of these primates and identified 22,758 hypomethylated and 15,858 hypermethylated human s-DMRs. These s-DMRs are globally enriched within weak promoter, enhancer and transcribed regions via comparison with ChromHMM segmentation. Human s-DMRs, (both hypo- and hypermethylated) are found to be more prevalent in CpG Island shores than within the islands themselves (?2 P = 1.80 x 10-32). Examining human-specific Transcription Factor Binding Site motif change within CpG islands, we show gain and loss, in hypomethylated and hypermethylated s-DMRs, respectively, of CTCF motifs. Epigenetically the most divergent human-specific locus was the immunological Leukotriene B4 receptor (LTB4R, aka BLT1 receptor), due to collocating hypomethylated s-DMRs within the promoter CpG island and shore, as well as inverse increased gene body methylation. This gene is vital in host immune responses and associated with the pathogenesis of a wide range of human inflammatory diseases. This finding was supported by additional neutrophil-only DNA methylome and lymphoblastoid H3K4me3 chromatin comparative data. Functional investigation of the consequences of these epigenetic differences identified this receptor to have increased expression, and have a higher response to the LTB4 ligand in human versus rhesus macaque peripheral blood mononuclear cells. This result further emphasises the exclusive nature of the human immunological system, its divergent adaptation even from closely related primates, and the power of comparative epigenomics to identify and understand human uniqueness. DNA methylome analysis of pooled Human, Chimpanzee and Macaque
2014-02-01 | E-GEOD-48942 | biostudies-arrayexpress
Project description:Purpose: We characterized genome-wide DNA methylation profiles (methylome) in purified peripheral blood monocytes (PBMs) from 18 healthy postmenopausal Caucasian females aged 50-56 years. Methods: DNA methylome of Human Peripheral Blood Monocytes were generated by methylated DNA immunoprecipitation combined with high-throughput sequencing (MeDIP-seq), using Illumina GAIIx. The sequence reads that passed quality filters were analyzed using MEDIPS package. Targeted methylation validation analysis was performed by using MassARRAY EpiTYPER assays. Genome-wide gene expression profiles have been obtained for 7 of the 18 subjects by using Affymetrix 1.0 Human Exon ST arrays following the manufacturer's recommended protocols. Results: Using MeDIP-seq,a total of approximately 283 million reads were uniquely aligned to human genome (Build NCBI37, HG19), resulting in average ~16 million uniquely aligned high quality reads per sample. Distinct patterns were revealed at different genomic features. For instance, promoters were commonly (~58%) found to be unmethylated; whereas protein coding regions were largely (~84%) methylated. We found that approximately 24% CpG islands (CGIs) were highly methylated in PBMs. Further characterization of CGIs with respect to their relative locations to RefSeq genes revealed that the highly methylated CGIs were largely enriched (~89%) in CGIs located in gene bodies and intergenic regions. By integration of the methylome data with genome-wide PBM gene expression data, we found negative correlation between promoter methylation levels and gene transcription levels when comparing groups of genes with different expression levels, and this relationship was consistently observed across promoters with high to low CpG densities. Furthermore, we observed a modest but significant excess (permutation p<0.0001) of genes showing negative correlation between inter-individual promoter methylation and transcription levels, particularly for genes associated with CpG-rich promoters. Across the 18 individual PBM methylomes, we also identified genomic regions that were constitutively highly methylated in PBMs as well as regions showing large inter-individual variability. Conclusions: This study represents a comprehensive analysis of the PBM methylome and our data provides a valuable resource for future epigenomic and multi-omic studies exploring biological and disease-related regulatory mechanisms in PBMs. DNA methylome of human peripheral blood monocytes were generated by MeDIP-seq, using Illumina GAIIx.
2013-07-24 | E-GEOD-39604 | biostudies-arrayexpress
Project description:Intestinal DNA methylome of preterm pigs
| PRJNA423044 | ENA