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DNA Methylation Protocols

Overview of attention for book
Cover of 'DNA Methylation Protocols'

Table of Contents

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    Book Overview
  2. Altmetric Badge
    Chapter 1 A Summary of the Biological Processes, Disease-Associated Changes, and Clinical Applications of DNA Methylation
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    Chapter 2 Considerations for Design and Analysis of DNA Methylation Studies
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    Chapter 3 Quantification of Global DNA Methylation Levels by Mass Spectrometry
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    Chapter 4 Antibody-Based Detection of Global Nuclear DNA Methylation in Cells, Tissue Sections, and Mammalian Embryos
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    Chapter 5 Whole-Genome Bisulfite Sequencing Using the Ovation® Ultralow Methyl-Seq Protocol
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    Chapter 6 Tagmentation-Based Library Preparation for Low DNA Input Whole Genome Bisulfite Sequencing
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    Chapter 7 Post-Bisulfite Adaptor Tagging for PCR-Free Whole-Genome Bisulfite Sequencing
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    Chapter 8 Multiplexed Reduced Representation Bisulfite Sequencing with Magnetic Bead Fragment Size Selection
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    Chapter 9 Low Input Whole-Genome Bisulfite Sequencing Using a Post-Bisulfite Adapter Tagging Approach
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    Chapter 10 Methyl-CpG-Binding Domain Sequencing: MBD-seq
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    Chapter 11 The HELP-Based DNA Methylation Assays
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    Chapter 12 Comprehensive Whole DNA Methylome Analysis by Integrating MeDIP-seq and MRE-seq
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    Chapter 13 Digital Restriction Enzyme Analysis of Methylation (DREAM)
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    Chapter 14 Nucleosome Occupancy and Methylome Sequencing (NOMe-seq)
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    Chapter 15 Bisulphite Sequencing of Chromatin Immunoprecipitated DNA (BisChIP-seq)
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    Chapter 16 A Guide to Illumina BeadChip Data Analysis
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    Chapter 17 Microdroplet PCR for Highly Multiplexed Targeted Bisulfite Sequencing
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    Chapter 18 Multiplexed DNA Methylation Analysis of Target Regions Using Microfluidics (Fluidigm)
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    Chapter 19 Large-Scale Targeted DNA Methylation Analysis Using Bisulfite Padlock Probes
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    Chapter 20 Targeted Bisulfite Sequencing Using the SeqCap Epi Enrichment System
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    Chapter 21 Multiplexed and Sensitive DNA Methylation Testing Using Methylation-Sensitive Restriction Enzymes “MSRE-qPCR”
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    Chapter 22 Quantitative DNA Methylation Analysis at Single-Nucleotide Resolution by Pyrosequencing®
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    Chapter 23 Methylation-Specific PCR
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    Chapter 24 Quantitation of DNA Methylation by Quantitative Multiplex Methylation-Specific PCR (QM-MSP) Assay
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    Chapter 25 MethyLight and Digital MethyLight
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    Chapter 26 Quantitative Region-Specific DNA Methylation Analysis by the EpiTYPER™ Technology
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    Chapter 27 Methylation-Specific Multiplex Ligation-Dependent Probe Amplification (MS-MLPA)
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    Chapter 28 Methylation-Sensitive High Resolution Melting (MS-HRM)
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    Chapter 29 Hairpin Bisulfite Sequencing: Synchronous Methylation Analysis on Complementary DNA Strands of Individual Chromosomes
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    Chapter 30 Helper-Dependent Chain Reaction (HDCR) for Selective Amplification of Methylated DNA Sequences
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    Chapter 31 DNA Methylation Analysis from Blood Spots: Increasing Yield and Quality for Genome-Wide and Locus-Specific Methylation Analysis
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    Chapter 32 DNA Methylation Analysis of Free-Circulating DNA in Body Fluids
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    Chapter 33 Tet-Assisted Bisulfite Sequencing (TAB-seq)
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    Chapter 34 Multiplexing for Oxidative Bisulfite Sequencing (oxBS-seq)
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    Chapter 35 Affinity-Based Enrichment Techniques for the Genome-Wide Analysis of 5-Hydroxymethylcytosine
Attention for Chapter 13: Digital Restriction Enzyme Analysis of Methylation (DREAM)
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  • High Attention Score compared to outputs of the same age and source (86th percentile)

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Chapter title
Digital Restriction Enzyme Analysis of Methylation (DREAM)
Chapter number 13
Book title
DNA Methylation Protocols
Published in
Methods in molecular biology, January 2018
DOI 10.1007/978-1-4939-7481-8_13
Pubmed ID
Book ISBNs
978-1-4939-7479-5, 978-1-4939-7481-8
Authors

Jaroslav Jelinek, Justin T. Lee, Matteo Cesaroni, Jozef Madzo, Shoudan Liang, Yue Lu, Jean-Pierre J. Issa, Jelinek, Jaroslav, Lee, Justin T., Cesaroni, Matteo, Madzo, Jozef, Liang, Shoudan, Lu, Yue, Issa, Jean-Pierre J.

Abstract

Digital Restriction Enzyme Analysis of Methylation (DREAM) is a method for quantitative mapping of DNA methylation across genomes using next-generation sequencing (NGS) technology. The method is based on sequential cuts of genomic DNA with a pair of restriction enzymes (SmaI and XmaI) at CCCGGG target sites. Unmethylated sites are first digested with SmaI. This enzyme cuts the sites in the middle at CCC^GGG, leaving behind blunt ended fragments. CpG methylation completely blocks SmaI; therefore, only unmethylated sites are cleaved. The remaining methylated sites are digested with XmaI in the next step. This enzyme is not blocked by CpG methylation. It cuts the recognition site sideways at C^CCGGG forming 5'-CCGG overhangs. The sequential cuts thus create distinct methylation-specific signatures at the ends of restriction fragments: 5'-GGG for unmethylated CpG sites and 5'-CCGGG for methylated sites. The DNA fragments resulting from the digestions are ligated to NGS adapters. Sequencing libraries are prepared using hexanucleotide barcodes for sample identification. Individual libraries with distinct barcodes are pooled and sequenced using a paired ends protocol. The sequencing reads are aligned to the genome and mapped to unique CCCGGG target sites. Methylation at individual CpG sites is calculated as the ratio of sequencing reads with the methylated signature to the total number of reads mapping to the site. Sequencing of 25 million reads per sample typically yields 50,000 unique CpG sites covered with hundreds of reads enabling accurate determination of DNA methylation levels. DREAM does not require bisulfite conversion, has a very low background, and has high sensitivity to low levels of methylation. The method is simple, cost-effective, quantitative, highly reproducible, and can be applied to any species.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 24 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 24 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 4 17%
Researcher 3 13%
Student > Postgraduate 2 8%
Student > Master 2 8%
Student > Doctoral Student 1 4%
Other 1 4%
Unknown 11 46%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 5 21%
Agricultural and Biological Sciences 3 13%
Medicine and Dentistry 2 8%
Nursing and Health Professions 1 4%
Veterinary Science and Veterinary Medicine 1 4%
Other 2 8%
Unknown 10 42%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 4. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 30 June 2022.
All research outputs
#7,302,639
of 24,093,053 outputs
Outputs from Methods in molecular biology
#2,187
of 13,601 outputs
Outputs of similar age
#140,860
of 449,849 outputs
Outputs of similar age from Methods in molecular biology
#203
of 1,480 outputs
Altmetric has tracked 24,093,053 research outputs across all sources so far. This one has received more attention than most of these and is in the 69th percentile.
So far Altmetric has tracked 13,601 research outputs from this source. They receive a mean Attention Score of 3.5. This one has done well, scoring higher than 83% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 449,849 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 68% of its contemporaries.
We're also able to compare this research output to 1,480 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 86% of its contemporaries.