نتایج جستجو برای: bisulfite sequencing
تعداد نتایج: 128044 فیلتر نتایج به سال:
Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis
We describe a large-scale random approach termed reduced representation bisulfite sequencing (RRBS) for analyzing and comparing genomic methylation patterns. BglII restriction fragments were size-selected to 500-600 bp, equipped with adapters, treated with bisulfite, PCR amplified, cloned and sequenced. We constructed RRBS libraries from murine ES cells and from ES cells lacking DNA methyltrans...
Background DNA methylation plays a key role in the regulation of gene expression and carcinogenesis. Bisulfite sequencing studies mainly focus on calling single nucleotide polymorphism, different methylation region, and find allele-specific DNA methylation. Until now, only a few software tools have focused on virus integration using bisulfite sequencing data. Findings We have developed a new ...
Summary: Bisulfite sequencing is the gold standard method for analyzing methylomes. However, the effect of quality control in bisulfite sequencing has not been studied extensively. We developed a package ME-Plot to detect the errors in bisulfite sequencing mapping data and produce higher quality methylation calls by trimming low quality portions of the reads. Our simulation results on both rand...
Summary: Sodium bisulfite conversion followed by sequencing (BSSeq, such as whole genome bisulfite sequencing or reduced representation bisulfite sequencing) has become popular for studying human epigenetic profiles. Identifying single nucleotide polymorphisms (SNPs) is important for quantification of methylation levels and for study of allele-specific epigenetic events such as imprinting. Howe...
DNA methylation pattern mapping is heavily studied in normal and diseased tissues. A variety of methods have been established to interrogate the cytosine methylation patterns in cells. Reduced representation of whole genome bisulfite sequencing was developed to detect quantitative base pair resolution cytosine methylation patterns at GC-rich genomic loci. This is accomplished by combining the u...
Deep sequencing after bisulfite conversion (BS-Seq) is the method of choice to generate whole genome maps of cytosine methylation at single base-pair resolution. Its application to genomic DNA of Arabidopsis flower bud tissue resulted in the first complete methylome, determining a methylation rate of 6.7% in this tissue. BS-Seq reads were mapped onto an in silico converted reference genome, app...
This SnapShot depicts key sequencing-based methods used in the analysis of epigenomes, including (1)bisulfite sequencing, (2) chromatin immunoprecipiation sequencing, (3) determination of open chromatin, and (4) 3D chromatin capture.
DNA methylation at cytosines is a widely studied epigenetic modification. Methylation is commonly detected using bisulfite modification of DNA followed by PCR and additional techniques such as restriction digestion or sequencing. These additional techniques are either laborious, require specialized equipment, or are not quantitative. Here we describe a simple algorithm that yields quantitative ...
High-throughput DNA sequencing technologies make it possible to determine the order of the nucleotides adenine, cytosine, guanine and thymine in DNA samples, resulting in millions of short strings (reads) over the alphabet (A, C, G, T). Advances in biological and biomedical research rely on the ability of bioinformatics to make sense out of that data with novel algorithms and tools. In this the...
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