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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 4: Antibody-Based Detection of Global Nuclear DNA Methylation in Cells, Tissue Sections, and Mammalian Embryos
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Chapter title
Antibody-Based Detection of Global Nuclear DNA Methylation in Cells, Tissue Sections, and Mammalian Embryos
Chapter number 4
Book title
DNA Methylation Protocols
Published in
Methods in molecular biology, January 2018
DOI 10.1007/978-1-4939-7481-8_4
Pubmed ID
Book ISBNs
978-1-4939-7479-5, 978-1-4939-7481-8
Authors

Nathalie Beaujean, Juliette Salvaing, Nur Annies Abd Hadi, Sari Pennings

Abstract

Immunostaining is widely used in cell biology for the in situ detection of proteins in fixed cells. The method is based on the specificity of antibodies for recognizing and binding to a selected target, combined with immunolabeling techniques for microscopic imaging. Antibodies with high specificities for modified nucleotides have also been widely developed, and among those, antibodies that recognize modified cytosine: 5-methylcytosine (5mC), and more recently, its derivates 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). To allow for their detection, primary antibody signals can be amplified using secondary antibodies coupled to fluorophores for immunofluorescence, or other molecules for immunocytochemistry.Immunostaining can be used to gain information on the spatial distribution and levels of DNA methylation states within the nucleus. Although the resolution remains quite low in genomic terms, advanced microscopy techniques and image analysis can obtain detailed spatial information content from immunostained sites. The technique complements genomic approaches that permit the assessment of DNA methylation on specific sequences, but that cannot provide global nuclear spatial context. Immunostaining is an accessible method of great benefit in several cases: when working with limited material (such as embryos or primary cells), to quickly assess at the level of individual cells the effect of siRNA, drugs, or biological processes that promote or inhibit DNA methylation or demethylation, or to study the 3D nuclear organization of regions with high DNA methylation, such as constitutive heterochromatin.Here, we review and outline protocols for the fluorescent and enzymatic immunodetection of DNA methylation in the nuclei of cells, tissue sections, and mammalian embryos.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 19 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 19 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 4 21%
Researcher 3 16%
Student > Bachelor 2 11%
Student > Master 2 11%
Professor 1 5%
Other 3 16%
Unknown 4 21%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 6 32%
Agricultural and Biological Sciences 4 21%
Unspecified 1 5%
Nursing and Health Professions 1 5%
Business, Management and Accounting 1 5%
Other 2 11%
Unknown 4 21%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 2. 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 22 December 2017.
All research outputs
#15,075,693
of 24,716,872 outputs
Outputs from Methods in molecular biology
#4,235
of 13,880 outputs
Outputs of similar age
#239,333
of 453,077 outputs
Outputs of similar age from Methods in molecular biology
#399
of 1,486 outputs
Altmetric has tracked 24,716,872 research outputs across all sources so far. This one is in the 38th percentile – i.e., 38% of other outputs scored the same or lower than it.
So far Altmetric has tracked 13,880 research outputs from this source. They receive a mean Attention Score of 3.5. This one has gotten more attention than average, scoring higher than 69% 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 453,077 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 46th percentile – i.e., 46% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 1,486 others from the same source and published within six weeks on either side of this one. This one has gotten more attention than average, scoring higher than 72% of its contemporaries.