Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Nanopore DNA sequencing in a model of oxidative stress

ABSTRACT: Cytosine DNA methylation in the CpG context (5mCpG) is associated with the transcriptional status of nuclear DNA. Due to technical limitations, it has been less clear if mitochondrial DNA (mtDNA) is methylated and whether 5mCpG has a regulatory role in this context. The main aim of this work was to develop and validate a novel tool for determining methylation of mtDNA and to corroborate its existence across different biological contexts. Here, we profiled the human cell lineHEK 293T, before and after oxidative stress, using long-read nanopore sequencing.

ORGANISM(S): Homo sapiens

PROVIDER: GSE159582 | GEO | 2021/04/20

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Nanopore DNA sequencing of a human liver progenitor-like cell line

Project description:Cytosine DNA methylation in the CpG context (5mCpG) is associated with the transcriptional status of nuclear DNA. Due to technical limitations, it has been less clear if mitochondrial DNA (mtDNA) is methylated and whether 5mCpG has a regulatory role in this context. The main aim of this work was to develop and validate a novel tool for determining methylation of mtDNA and to corroborate its existence across different biological contexts. Here, we profiled the human hepatocyte-like progenitor cell line HepaRG, before and after in vitro differentiation, using long-read nanopore sequencing.

2021-04-20 | GSE158224 | GEO

Native single molecule sequencing and de novo assembly of Hepatitis B Virus to detect 5mCpG

Project description:Methylation of Hepatitis B Virus (HBV) DNA in a CpG context (5mCpG) can alter the expression patterns of viral genes related to infection and cellular transformation. Moreover, it may also provide clues to why certain infections are cleared, or persist with or without progression to cancer. The detection of 5mCpG often requires techniques that damage DNA or introduce bias through a myriad of limitations. Therefore, we developed a method for the detection of 5mCpG on the HBV genome that does not rely on bisulfite conversion or PCR. Moreover, using the developed technique, we have provided the first de novo assembly of native HBV DNA, as well as the first landscape of 5mCpG from native HBV sequences

2021-01-05 | GSE162518 | GEO

Single molecule DNA methylation reveals unique epigenetic identity profiles of T helper cells

Project description:Identity and plasticity of CD4 T helper (Th) cells are regulated in part by epigenetic mechanisms. Cytosine methylation in CpG context (5mCpG) and cytosine hydroxymethylation (5hmCpG) are DNA modifications that identify stable cell phenotypes. To assess transition states in Th cells, we developed a method based on Cas9-targeted single molecule nanopore sequencing and found that 5mCpG can be used as markers of cellular identity. Targeting as few as 10 mouse selected genomic loci, we were able to distinguish major differentiated T cell subtypes as well as intermediate phenotypes by their native DNA 5mCpG patterns. Moreover, by using off-target sequences we were able to infer transcription factor activities relevant to each cell subtype. Our data highlight the potential to exploit native DNA methylation profiling to study physiological and pathological Th transition states.

2024-01-08 | GSE248540 | GEO

Epigenome of three deep-sea polychaete species

Project description:We provide the genome-wide methylome surveys of three species of deep-sea polychaete worms using Oxford Nanopore data: the siboglinids Paraescarpia echinospica and Ridgeia piscesae, and the alvinellid Paralvinella palmiformis. We characterised 5mCpG methylation in order to test hypotheses about the putative role of DNA methylation in these species.

2022-11-06 | GSE217309 | GEO

Targeted nanopore resequencing and methylation analysis of LINE-1 retrotransposons

Project description:We used the nanopore Cas9 targeted sequencing (nCATS) strategy to specifically sequence 125 L1HS-containing loci in parallel and measure their DNA methylation levels using nanopore long-read sequencing. Each targeted locus is sequenced at high coverage (~45X) with unambiguously mapped reads spanning the entire L1 element, as well as its flanking sequences over several kilobases. The genome-wide profile of L1 methylation was also assessed by bs-ATLAS-seq in the same cell lines (E-MTAB-10895).

2023-09-22 | E-MTAB-12247 | biostudies-arrayexpress

Systematic comparison of tools used for m6A mapping from nanopore direct RNA sequencing

Project description:State-of-the-art algorithms for m6A detection and quantification via nanopore direct RNA sequencing have been continuously developed, little is known about their capacities and limitations, which makes a comprehensive assessment in urgent need. Therefore, we performed comprehensive benchmarking of 10 computational tools relying on current-based and base-calling “errors” strategies for m6A detection by nanopore sequencing.

2023-03-01 | GSE195618 | GEO

Nanopore sequencing and data analysis for base-resolution genome-wide 5-methylcytosine profiling

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

Comparison of CcrM-dependent methylation in Caulobacter crescentus and Brucella abortus by nanopore sequencing

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

Nanopore DNA methylation analysis of brain tumors

Project description:Nanopore DNA methylation analysis of brain tumors

| PRJEB44439 | ENA

Nanopore DNA methylation analysis of brain tumors

Project description:Nanopore DNA methylation analysis of brain tumors

| PRJEB48142 | ENA