Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Enhanced methylome sequencing by recovery of unsequenceable fragments

ABSTRACT: Bisulfite sequencing is a valuable tool for mapping the position of 5-methylcytosine in the genome at single base resolution. However, the associated chemistry renders the majority of DNA fragments unsequenceable, thus necessitating PCR amplification. Furthermore, bisulfite conversion generates an A,T-rich DNA library that leads to major PCR biases that may confound methylation analysis. Here we report a method that enables accurate methylation analysis, by rebuilding the damaged DNA library after bisulfite treatment. This recovery after bisulfite treatment (ReBuilT) approach enables PCR-free bisulfite sequencing from low nanogram quantities of genomic DNA. We applied the ReBuilT method for whole methylome analysis of the A,T rich genome of Plasmodium berghei. We demonstrate substantial improvements in coverage and the reduction of sequence-context biases as compared to classical methylome analysis. Our method will be widely applicable for accurate, quantitative methylation analysis, even for technically challenging genomes, and where limited sample DNA is available.

ORGANISM(S): Plasmodium berghei ANKA

PROVIDER: GSE65116 | GEO | 2016/03/16

SECONDARY ACCESSION(S): PRJNA273015

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Enhanced methylome sequencing by recovery of unsequenceable fragments

Project description:Bisulfite sequencing is a valuable tool for mapping the position of 5-methylcytosine in the genome at single base resolution. However, the associated chemistry renders the majority of DNA fragments unsequenceable, thus necessitating PCR amplification. Furthermore, bisulfite conversion generates an A,T-rich DNA library that leads to major PCR biases that may confound methylation analysis. Here we report a method that enables accurate methylation analysis, by rebuilding the damaged DNA library after bisulfite treatment. This recovery after bisulfite treatment (ReBuilT) approach enables PCR-free bisulfite sequencing from low nanogram quantities of genomic DNA. We applied the ReBuilT method for whole methylome analysis of the A,T rich genome of Plasmodium berghei. We demonstrate substantial improvements in coverage and the reduction of sequence-context biases as compared to classical methylome analysis. Our method will be widely applicable for accurate, quantitative methylation analysis, even for technically challenging genomes, and where limited sample DNA is available. From the same DNA sample we prepared 3 PCR-free Bisulfite-Seq replicates (ReBuilT) and 2 standard Bisulfite-Seq replicates (PCR-BS).

2016-03-16 | E-GEOD-65116 | biostudies-arrayexpress

Clinical Study of Pan-cancer DNA Methylation Test in Plasma

Project description:We intend to establish an efficient method for plasma cfDNA extraction and Bisulfite transformation to facilitate the detection of DNA methylation status using multiplex fluorescence PCR. Meanwhile, we expect to identify several plasma methylation markers that can be highly sensitive for multi-cancer detection. Finally, we will provide a pan-cancer blood test that is easy to operate, low cost, accurate and easy to promote.

| 5068 | ecrin-mdr-crc

Efficient and accurate determination of genome-wide DNA methylation patterns in Arabidopsis thaliana with enzymatic methyl sequencing

Project description:5′ methylation of cytosines in DNA molecules is an important epigenetic mark in eukaryotes. Bisulfite sequencing is the gold standard of DNA methylation detection, and whole-genome bisulfite sequencing (WGBS) has been widely used to detect methylation at single-nucleotide resolution on a genome-wide scale. However, sodium bisulfite is known to severely degrade DNA, which, in combination with biases introduced during PCR amplification, leads to unbalanced base representation in the final sequencing libraries. Enzymatic conversion of unmethylated cytosines to uracils can achieve the same end product for sequencing as does bisulfite treatment and does not affect the integrity of the DNA; enzymatic methylation sequencing may, thus, provide advantages over bisulfite sequencing.

2020-10-07 | GSE151616 | GEO

DIRECT: Digital Microfluidics for Isolation-Free Shared Library Construction of Single-Cell DNA Methylome and Transcriptome

Project description:Integrated single-cell transcriptome and DNA methylome profiling has provided insight into the complex regulatory networks of cells. Existing methods are based on picking a single-cell and performing library construction in a tube, which is costly and cumbersome. Here, we propose DIRECT, a digital microfluidics-based method for simultaneous analysis of the methylome and transcriptome in a single library construction. The accuracy of DIRECT is demonstrated in comparison with bulk and single-omics data, and the high CpG site coverage of DIRECT allows for precise analysis of copy number variation information, enabling expansion of single cell analysis from two- to three-omics. By applying DIRECT to monitor the dynamics of mouse embryonic stem cell differentiation, the relationship between DNA methylation and changes in gene expression during differentiation was revealed. DIRECT enables accurate, robust, and reproducible single-cell DNA methylation and gene expression co-analysis at a lower cost and with greater efficiency, broadening the application scenarios of single-cell multi-omics analysis and revealing a more comprehensive and fine-grained map of cellular regulatory landscapes.

2023-08-10 | GSE240579 | GEO

Bisulfite-free epigenomics and genomics of single cells analyzed by methylation sensitive restriction (epi-gSCAR)

Project description:Single-cell multi-omics are powerful means to study cell-to-cell heterogeneity. Here, we present a single-tube, bisulfite-free method for the simultaneous, genome-wide analysis of DNA methylation and genetic variants in single cells: epigenomics and genomics of single cells analyzed by restriction (epi-gSCAR). By applying this method, we obtained DNA methylation measurements of up to 506,063 CpGs and up to 1,244,188 single-nucleotide variants from single leukemia-derived cells. We demonstrate that epi-gSCAR generates accurate and reproducible measurements of DNA methylation and allows to differentiate between two cell lines based on the DNA methylation and genetic profiles.

2020-10-28 | GSE131723 | GEO

Genome-wide profiling of DNA methylation at single-base resolution based on MeDIP-bisulfite high-throughput sequencing and ridge regression (MB)

Project description:Unraveling complexity of DNA methylome is essential to decipher DNA methylation mechanism in life. However, this has been subjected to technological constraints to balance between cost and accurate measurement of the DNA methylation level. In this study, by innovatively introducing C-hydroxylmethylated adapters, we have developed MeDIP-Bisulfite sequencing (MB-seq), which could obtain DNA methylome of repertoire CpGs at single-base resolution. We found MB-seq only costs 10% of MethylC-seq, but covers 85% of total CpGs in human genome. Unlike absolute methylation levels determined by MethylC-seq and RRBS, MB-seq presented relative methylation levels that are linearly inflated. This has enlightened us to develop a MB-seq corresponding correction method for methylation level based on ridge regression, which integrates the data of MB-seq and RRBS to predict the methylation level of total 28.2 million CpGs on human genome with high accuracy (Pearson correlation coefficient, PCC=0.90). Moreover, by employing MB-seq, we generated the DNA methylome of an ovarian epithelial cell line (T29) and its oncogenic counterpart (T29H), respectively. After ridge regression, we identified 131,790 differential methylation regions (DMRs) with high accuracy between T29 and T29H, far more than 7,567 obtained from RRBS. Taken together, our result demonstrated that the MB-seq combined with ridge regression is a wide applicable approach for profiling of DNA methylome.

2015-10-01 | GSE62279 | GEO

Genome-wide profiling of DNA methylation at single-base resolution based on MeDIP-bisulfite high-throughput sequencing and ridge regression (MethyC + MeDIP)

2015-10-01 | GSE62277 | GEO

Genome-wide profiling of DNA methylation at single-base resolution based on MeDIP-bisulfite high-throughput sequencing and ridge regression (RNA)

2015-10-01 | GSE62276 | GEO

Simultaneous methylation-level assessment of hundreds of CpG sites by targeted bisulfite PCR sequencing (TBPseq)

Project description:Methylated-DNA sequencing technologies are producing vast amounts of methylome data from cancer samples, from which cancer-associated differentially methylated CpG sites (cDMCs) are continuously identified and filed. The inclusion of as many cDMCs as possible helps improve the accuracy of cancer diagnosis and sometimes identify cancer subtypes. However, the lack of an established method for the analysis of hundreds of cDMCs practically impedes their robust use in clinical medicine. Here, we tested the availability of targeted bisulfite-PCR-sequencing (TBPseq) technology for the assessment of methylation levels of a myriad of CpGs scattered over the genome. In randomly selected 46 cancer cell lines, multiplexed PCR yielded a variety of amplicons harboring 250 CpGs residing at promoters of 97 cancer-associated genes, all of which were sequenced in the same flow cell. Clustering analysis of the TBPseq-assessed methylation levels of target CpGs showed that the lung and liver cancer cell lines correlated relatively strongly with each other while they weakly correlated with colon cancer cells. CpGs at the MLH1 gene promoter, which are known to be hypermethylated in colon cancers, indeed were heavily methylated in the tested colon cancer cells. LIFR CpGs, also known to be methylated in colon cancers, were hypermethylated in the colon cancer cells. Moreover, MLH1 and LIFR promoter hypermethylations were found in colon cancer cells only, but not in biliary tract, liver, lung and stomach cancers cell lines. A meta-analysis with public cancer methylome datasets verified the colorectal cancer specificity of MLH1 and LIFR promoter methylation. These results demonstrate that our TBPseq-based methylation assessment could be considered an effective, accurate, and competitive method to simultaneously examine a large number of target cDMCs and patient samples.

2018-05-01 | GSE98921 | GEO

DNA 5-methylcytosine specific profiling with limited input

Project description:DNA methylation 5mC specific detection has been limited by the mixed signals from traditional bisulfite sequencing or by the severe degradation of input during oxBS-seq pretreatment. Here, we presented a 5mC specific whole genome amplification method (5mC-WGA), with which we achieved whole genome bisulfite sequencing with 5mC retention from limited input down to 10 pg scale without 5hmC signals, presenting DNA 5mC methylome with high producibility and great accuracy.

2020-04-14 | GSE112875 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data