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DNA Methylation Protocols

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

Table of Contents

  1. Altmetric Badge
    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 33: Tet-Assisted Bisulfite Sequencing (TAB-seq)
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  • High Attention Score compared to outputs of the same age and source (84th percentile)

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Chapter title
Tet-Assisted Bisulfite Sequencing (TAB-seq)
Chapter number 33
Book title
DNA Methylation Protocols
Published in
Methods in molecular biology, January 2018
DOI 10.1007/978-1-4939-7481-8_33
Pubmed ID
29224168
Book ISBNs
978-1-4939-7479-5, 978-1-4939-7481-8
Authors

Miao Yu, Dali Han, Gary C. Hon, Chuan He, Yu, Miao, Han, Dali, Hon, Gary C., He, Chuan

Abstract

5-Hydroxymethylcytosine (5hmC) is a modified form of cytosine, which has recently been found in mammalian cells and tissues. 5hmC is derived from 5-methylcytosine (5mC) by Ten-eleven translocation (TET) family protein-mediated oxidation and may regulate gene expression. Numerous affinity-based profiling methods have been developed to help understand the exact function of 5hmC in the genome. However, these methods have a relatively low resolution (~100 bp) without quantitative information of the modification percentage on each site. Here we demonstrated the detailed procedure of Tet-Assistant Bisulfite Sequencing (TAB-Seq), which can detect 5hmC at single-base resolution and quantify its abundance at each site. In this protocol, the genomic DNA is first treated with βGT and recombinant mTet1 consecutively to convert 5hmC to 5gmC and 5mC to 5caC, respectively. The treated genomic DNA can be directly applied to bisulfite treatment to detect 5hmC on specific loci or applied to whole-genome bisulfite sequencing as needed.

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X Demographics

The data shown below were collected from the profile of 1 X user who shared this research output. Click here to find out more about how the information was compiled.
 Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 45 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 45 100%

Demographic breakdown

Readers by professional status Count As %
Student > Master 5 11%
Student > Doctoral Student 4 9%
Student > Bachelor 3 7%
Researcher 2 4%
Professor > Associate Professor 2 4%
Other 5 11%
Unknown 24 53%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 13 29%
Agricultural and Biological Sciences 2 4%
Medicine and Dentistry 2 4%
Chemistry 2 4%
Neuroscience 1 2%
Other 1 2%
Unknown 24 53%
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 29 June 2023.
All research outputs
#8,060,551
of 24,911,633 outputs
Outputs from Methods in molecular biology
#2,429
of 13,988 outputs
Outputs of similar age
#152,832
of 454,154 outputs
Outputs of similar age from Methods in molecular biology
#227
of 1,485 outputs
Altmetric has tracked 24,911,633 research outputs across all sources so far. This one has received more attention than most of these and is in the 66th percentile.
So far Altmetric has tracked 13,988 research outputs from this source. They receive a mean Attention Score of 3.5. This one has done well, scoring higher than 81% 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 454,154 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 65% of its contemporaries.
We're also able to compare this research output to 1,485 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 84% of its contemporaries.

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