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Reduced Representation Bisulfite Sequencing (RRBS)
Reduced representation bisulfite sequencing (RRBS) enriches CpG-rich genomic regions using the MspI restriction enzyme—which cuts DNA at all CCGG...
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bsgenova: an accurate, robust, and fast genotype caller for bisulfite-sequencing data
BackgroundBisulfite sequencing (BS-Seq) is a fundamental technique for characterizing DNA methylation profiles. Genotype calling from...
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Ultrafast bisulfite sequencing detection of 5-methylcytosine in DNA and RNA
Bisulfite sequencing (BS-seq) to detect 5-methylcytosine (5mC) is limited by lengthy reaction times, severe DNA damage, overestimation of 5mC level...
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LABS: linear amplification-based bisulfite sequencing for ultrasensitive cancer detection from cell-free DNA
Methylation-based liquid biopsies show promises in detecting cancer using circulating cell-free DNA; however, current limitations impede clinical...
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Optimized bisulfite sequencing analysis reveals the lack of 5-methylcytosine in mammalian mitochondrial DNA
BackgroundDNA methylation is one of the best characterized epigenetic modifications in the mammalian nuclear genome and is known to play a...
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Next-Generation Bisulfite Sequencing for Targeted DNA Methylation Analysis
Bisulfite sequencing is the “gold-standard” technique for DNA methylation analysis. By combining bisulfite sequencing with high-throughput,...
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Hairpin-Bisulfite PCR
Ligation of a hairpin oligonucleotide to genomic DNA prior to bisulfite conversion and PCR amplification physically links the two complementary DNA...
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Anchor-based bisulfite sequencing determines genome-wide DNA methylation
Whole Genome Bisulfite Sequencing (WGBS) is the current standard for DNA methylation profiling. However, this approach is costly as it requires...
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Whole-Genome Bisulfite Sequencing for Detection of DNA Methylation in Crops
DNA methylations are well known for their regulatory functions and involved in various biological processes. Due to its great importance, the...
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A pipeline for sample tagging of whole genome bisulfite sequencing data using genotypes of whole genome sequencing
BackgroundIn large-scale high-throughput sequencing projects and biobank construction, sample tagging is essential to prevent sample mix-ups. Despite...
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DNA Methylation Analysis Using Bisulfite Pyrosequencing
Pyrosequencing is a DNA sequencing-by-synthesis technique that can quantitatively detect single-nucleotide polymorphisms (SNPs). With pyrosequencing,...
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Manipulating base quality scores enables variant calling from bisulfite sequencing alignments using conventional bayesian approaches
BackgroundCalling germline SNP variants from bisulfite-converted sequencing data poses a challenge for conventional software, which have no inherent...
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Strengths and limitations of reduced representation bisulfite sequencing (RRBS) in the perspective of DNA methylation analysis in fish: a case-study on rainbow trout spermatozoa
DNA methylation in CpG dinucleotides is an important epigenetic mark in fish spermatozoa since it has been shown that some sperm methylome features...
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Post-bisulfite Adaptor Tagging with a Highly Efficient Single-Stranded DNA Ligation Technique
Post-bisulfite adaptor tagging (PBAT) is a procedure for efficiently preparing a sequencing library for whole-genome bisulfite sequencing (WGBS). The...
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Post-bisulfite Adaptor Tagging Based on an ssDNA Ligation Technique (tPBAT)
Post-bisulfite adaptor tagging (PBAT) is a concept that enables the preparation of an efficient sequencing library from bisulfite-treated DNA, and it...
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Whole-genome bisulfite sequencing identified the key role of the Src family tyrosine kinases and related genes in systemic lupus erythematosus
BackgroundAs a multisystemic autoimmune illness, the basic mechanisms behind the pathophysiology of systemic lupus erythematosus (SLE) remain poorly...
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Low-Input Whole-Genome Bisulfite Sequencing
DNA methylation can regulate gene expression by modulating chromatin accessibility and transcription factor binding on promoter and enhancer regions....
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Oxidative Bisulfite Sequencing: An Experimental and Computational Protocol
Bisulfite sequencing (BS-seq) remains the gold standard technique to quantitively map DNA methylation at a single-base resolution. However, BS-seq...
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Bioinformatics Analysis of DNA Methylation Through Bisulfite Sequencing Data
DNA methylation plays an important role in the regulation of gene expression as one of the epigenetic modifications. The bisulfite sequencing is...
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Analysis of Bisulfite Sequencing Data Using Bismark and DMRcaller to Identify Differentially Methylated Regions
The mechanism of the addition of a methyl group to cytosine has been identified as one of several heritable epigenetic mechanisms. In plants, DNA...