Ontology highlight
ABSTRACT:
PROVIDER: PRJNA812072 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Whole-genome bisulfite sequencing (WGBS) is currently the gold standard for DNA methylation (5-methylcytosine, 5mC) profiling, however the destructive nature of sodium bisulfite results in DNA fragmentation and subsequent biases in sequencing data. Such issues have led to the development of bisulfite-free methods for 5mC detection. Nanopore sequencing is a long read non-destructive approach that directly analyzes DNA and RNA fragments in real time. Recently, computational tools have been developed that enable base-resolution detection of 5mC from Oxford Nanopore sequencing data. In this chapter we provide a detailed protocol for preparation, sequencing, read assembly and analysis of genome-wide 5mC using Nanopore sequencing technologies.
2021-12-03 | GSE179673 | GEO
Project description:Real-time Monitoring of Cisplatin Toxicity on Cancer Cells
| PRJNA139373 | ENA
Project description:In this study, we compared the two long-read sequencing platforms, namely the single-molecule real-time sequencing by Pacific Biosciences and nanopore sequencing by Oxford Nanopore Technologies, for the analysis of cell-free DNA from plasma. Artificial mixtures of sonicated human and mouse DNA at different sizes were sequenced with the two platforms.
| EGAS00001006329 | EGA
Project description:Bornean orangutan; a critically endangered hominoid
| PRJNA28639 | ENA
Project description:The delta smelt (Hypomesus transpacificus) is a pelagic fish species endemic to the Sacramento-San Joaquin Estuary in Northern California, listed as endangered under both the USA Federal and Californian State Endangered Species Acts and acts as an indicator of ecosystem health in its habitat range. Interrogative tools are required to successfully monitor effects of contaminants upon the delta smelt, and to research potential causes of population decline in this species. We used microarray technology to investigate genome-wide effects in 47-day old larvae after a 7-day exposure to ambient water samples from the Sacramento River at a monitoring field station (Hood) situated 8 miles downstream of the Sacramento regional Wastewater Treatment Plant. Genomic assessments were carried out on surviving organisms and contrasted to laboratory controls.
2012-09-20 | GSE40991 | GEO
Project description:Bacteria rely on DNA methylation for restriction modification systems and for epigenetic control of gene expression. In Alphaproteobacteria, the CcrM orphan methyltransferase is particularly noteworthy in a range of transcriptional regulation. The wider adoption of nanopore sequencing and updated processing pipelines has made epigenome measurements in bacteria more convenient than before. Here, we validate this approach in Alphaproteobacteria by measuring CcrM-dependent DNA methylation in Caulobacter crescentus and show excellent correlation with other approaches. Continuing in Caulobacter, we directly measure the impact of Lon-mediated CcrM degradation on the epigenome and show that the AlkB demethylase has no global impact on DNA methylation during normal growth. We report on the global DNA methylation in Brucella abortus for the first time and find that CcrM-dependent methylation is reliant on Lon in an unexpected species- and chromosome-specific manner. Finally, we measure the impact of the MucR transcription factor on the Brucella methylome. Given the ease and reduced costs, our work demonstrates the utility of nanopore-based sequencing for epigenome monitoring in Alphaproteobacteria.
2024-03-11 | GSE260848 | GEO
Project description:The Oxford Nanopore (ONT) platform provides portable and rapid genome sequencing, and its ability to natively profile DNA methylation without complex sample processing is attractive for clinical sequencing. We recently demonstrated ONT shallow whole-genome sequencing to detect copy number alterations (CNA) from the circulating tumor DNA (ctDNA) of cancer patients. Here, we show that cell-type and cancer-specific methylation changes can also be detected, as well as cancer-associated fragmentation signatures. This feasibility study suggests that ONT shallow WGS could be a powerful tool for liquid biopsy, especially real-time medical applications.
2022-04-27 | GSE185307 | GEO