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Anchor-Based Bisulfite Sequencing determines genome-wide DNA methylation

ABSTRACT: Anchor-Based Bisulfite Sequencing determines genome-wide DNA methylation

PROVIDER: PRJNA749583 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15242562_1.fastq.gz	Fastqsanger.gz
	SRR15242562_2.fastq.gz	Fastqsanger.gz
	SRR15242563_1.fastq.gz	Fastqsanger.gz
	SRR15242563_2.fastq.gz	Fastqsanger.gz
	SRR15242564_1.fastq.gz	Fastqsanger.gz

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Anchor-Based Bisulfite Sequencing determines genome-wide DNA methylation

Project description:Whole Genome Bisulfite Sequencing (WGBS) is the current standard for DNA methylation profiling; however, WGBS is costly as it requires sequencing coverage over the entire genome. Here we introduce Anchor-Based Bisulfite Sequencing (ABBS). We show that ABBS captures accurate DNA methylation information in Escherichia coli and mammalian cells, while requiring approximately 20 times fewer sequencing reads than WGBS. The ABBS protocol is simple and can be performed in a single day.

2022-05-23 | GSE180796 | GEO

Anchor-based bisulfite sequencing determines genome-wide DNA methylation

Project description:Whole Genome Bisulfite Sequencing (WGBS) is the current standard for DNA methylation profiling. However, this approach is costly as it requires sequencing coverage over the entire genome. Here we introduce Anchor-Based Bisulfite Sequencing (ABBS). ABBS captures accurate DNA methylation information in Escherichia coli and mammals, while requiring up to 10 times fewer sequencing reads than WGBS. ABBS interrogates the entire genome and is not restricted to the CpG islands assayed by methods like Reduced Representation Bisulfite Sequencing (RRBS). The ABBS protocol is simple and can be performed in a single day. Anchor-Based Bisulfite Sequencing (ABBS) is a sequencing based method that enables analysis of DNA methylation states, based on specific hybridization of bisulfite-refractory methylcytosines with 8-aza-7-deaza-2-deoxyguanosine, incorporated in a primer at the end of 5 random nucleotides.

| S-EPMC9203462 | biostudies-literature

Genome-wide, High Resolution DNA Methylation Profiling Using Bisulfite-Mediated Cytosine Conversion

Project description:We developed a genome-wide DNA methylation profiling technology that determines methylation patterns using small amounts of starting material. This process involves a novel amplification step for DNA subjected to bisulfite-mediated cytosine conversion and generates highly reproducible datasets with low technical variation. The technology, named BiMP (for Bisulfite Methylation Profiling), is more cost-effective than mC immunoprecipitation techniques (mCIP) and can be applied to as little as 100 ng of Arabidopsis DNA. It is anticipated that this technology can be applied to mammalian genomes and may allow methylation profiling of a small number of physiologically uniform cells. Keywords: bisulfite DNA methylation profiling, Arabidopsis, methylation polymorphisms, met1-3,

2007-11-30 | GSE9051 | GEO

Tagmentation-based Whole Genome Bisulfite Sequencing

Project description:We demonstrated the reliability of the tagmentation-based whole genome bisulfite sequencing in direct comparison with the conventional whole genome bisulfite sequencing.

| EGAS00001000528 | EGA

The Histone Methyltransferase Wbp7 Controls Macrophage Function through GPI Glycolipid Anchor Synthesis

Project description:This SuperSeries is composed of the following subset Series: GSE30971: The Histone Methyltransferase Wbp7 Controls Macrophage Function through GPI Glycolipid Anchor Synthesis. [Expression Profile] GSE30972: The Histone Methyltransferase Wbp7 Controls Macrophage Function through GPI Glycolipid Anchor Synthesis. [ChIP_seq] Refer to individual Series

2012-04-08 | E-GEOD-30973 | biostudies-arrayexpress

Robust bisulfite free SMRT Sequencing of mdC based on a novel hpTet3-enzyme

Project description:Genomic DNA contains next to the four canonical nucleosides dA, dC, dG and T the additional base 5-methyldeoxycytidine (mdC). The presence of this methylated cytidine nucleoside in promoter regions or gene bodies has an instrumental effect on the transcriptional activity of the corresponding gene. The methylation patterns of genes are therefore responsible for either silencing or activation of genes. Sequencing of mdC positions in the genome is consequently of paramount importance for early cancer diagnostics in order to determine incorrect expression of genes. Today, the bisulfite method is the gold standard for mdC-sequencing, which has however the caveat that the majority of the input DNA is degraded during the bisulfite treatment. In addition, bisulfite sequencing is rather error prone. Here we report a benign, bisulfite free mdC sequencing method based on 3rd generation single molecule SMRT sequencing. The fundament of the technology is a new Tet3 enzyme that oxidizes mdCs with high efficiency to 5-carboxycytidine (cadC). caC in turn provides and excellent read out by SMRT sequencing using specially trained AI-based algorithms.

2024-11-20 | GSE256446 | GEO

Genome-wide quantitative analysis of DNA methylation from bisulfite sequencing data.

Project description:UnlabelledHere we present the open-source R/Bioconductor software package BEAT (BS-Seq Epimutation Analysis Toolkit). It implements all bioinformatics steps required for the quantitative high-resolution analysis of DNA methylation patterns from bisulfite sequencing data, including the detection of regional epimutation events, i.e. loss or gain of DNA methylation at CG positions relative to a reference. Using a binomial mixture model, the BEAT package aggregates methylation counts per genomic position, thereby compensating for low coverage, incomplete conversion and sequencing errors.Availability and implementationBEAT is freely available as part of Bioconductor at www.bioconductor.org/packages/devel/bioc/html/BEAT.html. The package is distributed under the GNU Lesser General Public License 3.0.

| S-EPMC4071208 | biostudies-literature

methylGrapher: Genome-Graph-Based Processing of DNA Methylation Data from Whole Genome Bisulfite Sequencing

Project description:methylGrapher: Genome-Graph-Based Processing of DNA Methylation Data from Whole Genome Bisulfite Sequencing

| PRJNA1086543 | ENA

LABS: linear amplification-based bisulfite sequencing for ultrasensitive cancer detection from cell-free DNA

Project description:Methylation-based liquid biopsies show promise in detecting cancer from circulating cell-free DNA, but current limitations impede clinical application. Most assays necessitate substantial DNA inputs, posing challenges. Underrepresented tumor DNA fragments may go undetected during exponential amplification steps of traditional sequencing methods. Here we report LABS (Linear Amplification based Bisulfite Sequencing), enabling linear amplification of bisulfite-treated DNA fragments in a genome-wide, unbiased fashion, detecting cancer abnormalities with sub-nanogram inputs. Applying LABS to 100 patient samples revealed cancer-specific patterns, copy number alterations, and enhanced cancer detection accuracy by identifying tissue-of-origin and immune cell composition.

2024-04-24 | GSE186007 | GEO

Genome-wide DNA methylation maps in follicular lymphoma cells determined by methylation-enriched bisulfite sequencing.

Project description:BackgroundFollicular lymphoma (FL) is a form of non-Hodgkin's lymphoma (NHL) that arises from germinal center (GC) B-cells. Despite the significant advances in immunotherapy, FL is still not curable. Beyond transcriptional profiling and genomics datasets, there currently is no epigenome-scale dataset or integrative biology approach that can adequately model this disease and therefore identify novel mechanisms and targets for successful prevention and treatment of FL.Methodology/principal findingsWe performed methylation-enriched genome-wide bisulfite sequencing of FL cells and normal CD19(+) B-cells using 454 sequencing technology. The methylated DNA fragments were enriched with methyl-binding proteins, treated with bisulfite, and sequenced using the Roche-454 GS FLX sequencer. The total number of bases covered in the human genome was 18.2 and 49.3 million including 726,003 and 1.3 million CpGs in FL and CD19(+) B-cells, respectively. 11,971 and 7,882 methylated regions of interest (MRIs) were identified respectively. The genome-wide distribution of these MRIs displayed significant differences between FL and normal B-cells. A reverse trend in the distribution of MRIs between the promoter and the gene body was observed in FL and CD19(+) B-cells. The MRIs identified in FL cells also correlated well with transcriptomic data and ChIP-on-Chip analyses of genome-wide histone modifications such as tri-methyl-H3K27, and tri-methyl-H3K4, indicating a concerted epigenetic alteration in FL cells.Conclusions/significanceThis study is the first to provide a large scale and comprehensive analysis of the DNA methylation sequence composition and distribution in the FL epigenome. These integrated approaches have led to the discovery of novel and frequent targets of aberrant epigenetic alterations. The genome-wide bisulfite sequencing approach developed here can be a useful tool for profiling DNA methylation in clinical samples.

| S-EPMC2947499 | biostudies-literature

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