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Methylation and Epigenetics Bioinformatic Tools - http://www.molecularstation.com/bioinformatics/link/Epigenetics_and_Methylation/

Category: Epigenetics and Methylation Protocols

Methylation database, CpG Island predictors, Methylation Primer design tools and databases. Epigenetic tools and bioinformatics. - [Read Methylation and Epigenetics Bioinformatic Tools]

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A practical guide to DNA methylation Promega PDF - http://www.promega.com/pnotes/42/methv3/Methv3_core.pdf

Category: Epigenetics and Methylation Protocols

The pattern and extent of DNA methylation can significantly affect the success of restriction digestions or bacterial transformations. Prokaryotic DNA may be methylated by host restriction/modification systems, while eukaryotic DNA often is methylated i - [Read A practical guide to DNA methylation Promega PDF]

A simple method for estimating global DNA methylation using bisulfite PCR of repetitive DNA elements - http://nar.oxfordjournals.org/cgi/content/full/32/3/e38

Category: Epigenetics and Methylation Protocols: Bisulfite Treatment Methylation Assay Protocol

Yang et al, NAR. 2004. ue to the heavy methylation of repetitive elements, this assay was especially useful in detecting decreases in DNA methylation, and this assay was validated by examining cell lines treated with the methylation inhibitor 5-aza-2'deox - [Read A simple method for estimating global DNA methylation using bisulfite PCR of repetitive DNA elements]

Analysis of DNA Methylation using Bisulphite Sequencing Protocol - http://www.methods.info/Methods/DNA_methylation/Bisulphite_sequencing.html

Category: PCR Protocols: Bisulfite Conversion Based PCR Protocols

Protocol for the analysis of DNA methylation using bisulphite sequencing. Method allows precise analysis of methylation in a certain region by converting all nonmethylated cytosines into tymines, while methylated cytosines remain unchanged. This method requires small amount of genomic DNA and therefore seems to be very useful for the analysis of clinical samples, where the material amount is limited.
- [Read Analysis of DNA Methylation using Bisulphite Sequencing Protocol]

Analysis of DNA Methylation using SnuPE Protocol - http://www.methods.info/Methods/DNA_methylation/methylation_snupe.pdf

Category: PCR Protocols: Bisulfite Conversion Based PCR Protocols

Protocol for analysis of DNA methylation using SnuPE. - [Read Analysis of DNA Methylation using SnuPE Protocol]

Analysis of methylation using bisulphite sequencing - http://www.methods.info/Methods/DNA_methylation/Bisulphite_sequencing.html

Category: Epigenetics and Methylation Protocols: Bisulfite Treatment Methylation Assay Protocol

This method allows precise analysis of methylation in a certain region by converting all nonmethylated cytosines into tymines, while methylated cytosines remain unchanged. Dr. A. Gratchev Methods.info - [Read Analysis of methylation using bisulphite sequencing]

Bisulfite Treatment of DNA Anderson Lab - http://www.mdanderson.org/departments/methylation/display.cfm?id=955D5740-37D4-444F-ACF0193F8EC3989B&method=displayFull&pn=A3F15D82-C9B4-41CD-BA4BE767E50A73D2

Category: Epigenetics and Methylation Protocols

Bisulfite Treatment of DNA Anderson Lab. Adapted from Frommer et.al. - [Read Bisulfite Treatment of DNA Anderson Lab]

Bisulfite Treatment of DNA for Methylation Analysis - http://www.mdanderson.org/departments/methylation/display.cfm?id=955D5740-37D4-444F-ACF0193F8EC3989B&method=displayFull

Category: Epigenetics and Methylation Protocols: Bisulfite Treatment Methylation Assay Protocol

Adapted from Frommer et.al. Good protocol for bisulfite treatment of DNA. Includes tips on Methylation PCR for CpG methylation analysis. University of Texas M. D. Anderson Cancer Center - [Read Bisulfite Treatment of DNA for Methylation Analysis]

Bisulfite-PCR for Restriction Analysis and/or Sequencing - http://www.mdanderson.org/departments/methylation/display.cfm?id=8E0AAAAC-FA42-486C-A93F60CD6E1C7E51&method=displayFull&pn=A3F15D82-C9B4-41CD-BA4BE767E50A73D2

Category: Epigenetics and Methylation Protocols

Bisulfite-PCR for Restriction Analysis and/or Sequencing. Protocol written by Jean-Pierre Issa. M.D Anderson Cancer Centre Texas. - [Read Bisulfite-PCR for Restriction Analysis and/or Sequencing]

Bisulfite-PCR for Restriction Analysis and/or Sequencing Protocol - http://www.mdanderson.org/departments/methylation/display.cfm?id=8E0AAAAC-FA42-486C-A93F60CD6E1C7E51&method=displayFull&pn=A3F15D82-C9B4-41CD-BA4BE767E50A73D2

Category: PCR Protocols: Bisulfite Conversion Based PCR Protocols

Protocol for bisulfite-PCR for restriction analysis and/or sequencing. Bisulfite-PCR followed by restriction is a rapid and semi-quantitative method of analyzing DNA methylation. The PCR products are also suitable for either direct sequencing or cloning and sequencing. The most important step here is primer selection. - [Read Bisulfite-PCR for Restriction Analysis and/or Sequencing Protocol]

Clonality - X Chromosome Inactivation Assay Protocol - http://cgap-mf.nih.gov/Protocols/DNARNAProteomicAnalysis/DNA/DNAProtocols/Clonality.html

Category: Genetics and Genomics: Cancer Genetics Protocols

Investigators can utilize X chromosome inactivation (methylation) to determine the clonality status of a tumor or premalignant lesion in females. The technique is based on a methylation-sensitive restriction enzyme and analysis of a polymorphic locus on the X chromosome. Clonal cell populations will show "loss" of the non-methylated allele after restriction digest. The assay can be performed on DNA recovered from microdissected samples. Both frozen tissue and fixed-embedded tissue can be used. - [Read Clonality - X Chromosome Inactivation Assay Protocol]

DNA-Methyltransferase Assay - Anderson Centre - http://www.mdanderson.org/departments/methylation/display.cfm?id=9B5B6082-C53A-4A86-BEE3EE149A52251E&method=displayFull&pn=A3F15D82-C9B4-41CD-BA4BE767E50A73D2

Category: Epigenetics and Methylation Protocols

M.D. Anderson Cancer Centre Texas - [Read DNA-Methyltransferase Assay - Anderson Centre]

DNA-Methyltransferase Assay Protocol - http://www.mdanderson.org/departments/methylation/display.cfm?id=9B5B6082-C53A-4A86-BEE3EE149A52251E&method=displayFull&pn=A3F15D82-C9B4-41CD-BA4BE767E50A73D2

Category: Nucleic Acid Modification Protocols: DNA Methylation Protocols

Protocol for DNA-methyltransferase assay. Includes: Homogenize Cells/Tissues; Quantitate Protein Concentration; Dilute Samples; The Assay Proper; Troubleshooting. - [Read DNA-Methyltransferase Assay Protocol]

Factors that Influence Restriction Enzyme Digestion Activity - http://arbl.cvmbs.colostate.edu/hbooks/genetics/biotech/enzymes/cuteffects.html

Category: Molecular Biology Protocols: Restriction Enzyme Digestion

Factors that Influence Restriction Enzyme Digestion Activity. Buffer Composition, Incubation Temperature, DNA Methylation, Star Activity, Multiple Enzymes. Laura Austgen PhD et. al, Biomedical Hypertextbook, Colorado State Univ. - [Read Factors that Influence Restriction Enzyme Digestion Activity]

Functional Analyses for Site-Specific Phosphorylation of a Target Protein in Cells - http://www.natureprotocols.com/2007/01/10/functional_analyses_for_sitesp.php

Category: Antibody Protocols: Antibody Production Protocols

Novel strategy of immunizing a phosphorylated peptide or a synthetic phosphopeptide, which corresponds to the protein phosphorylated at a targeted residue. Method has been applied to the production of antibodies that can specifically recognize the other types of site-specific protein modification, such as acetylation, methylation, and proteolysis. - [Read Functional Analyses for Site-Specific Phosphorylation of a Target Protein in Cells]

Linkage Analysis Using the NaOH Methylation Method Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/1/pdb.prot4249

Category: Chromatography Protocols: Gas Chromatography Protocols

Linkage analysis provides information on sugar type, ring size, and substitution positions for each monosaccharide. The method in this protocol, using NaOH as the base, is one of the simpler linkage analysis methods. It requires approximately 1-5 µg of carbohydrate. - [Read Linkage Analysis Using the NaOH Methylation Method Protocol]

Methods for Analyzing the Role of DNA Methylation and Chromatin Structure in Regulating T Lymphocyte - http://www.biologicalprocedures.com/bpo/arts/1/89/m89.pdf

Category: Nucleic Acid Modification Protocols: DNA Methylation Protocols

Methods for analyzing the role of DNA methylation and chromatin structure in regulating T lymphocyte gene expression. - [Read Methods for Analyzing the Role of DNA Methylation and Chromatin Structure in Regulating T Lymphocyte]

Methylated CpG Island Amplification - http://www.mdanderson.org/departments/methylation/display.cfm?id=8A198378-986B-41FD-8778FA1399FBAB4D&method=displayFull&pn=A3F15D82-C9B4-41CD-BA4BE767E50A73D2

Category: Epigenetics and Methylation Protocols

Methylated CpG Island Amplification. Protocol written by Minoru Toyota. M.D Anderson Cancer Centre Texas. - [Read Methylated CpG Island Amplification]

Methylated CpG Island Amplification Protocol - http://www.mdanderson.org/departments/methylation/display.cfm?id=8A198378-986B-41FD-8778FA1399FBAB4D&method=displayFull&pn=A3F15D82-C9B4-41CD-BA4BE767E50A73D2

Category: PCR Protocols: Bisulfite Conversion Based PCR Protocols

Protocol for methylated CpG island amplification. - [Read Methylated CpG Island Amplification Protocol]

Methylation Interference Protocol - http://genetics.med.harvard.edu/~cepko/protocol/mike/M1.html

Category: DNA Protein Interactions Protocols

Protocol for methylation interference. - [Read Methylation Interference Protocol]

Methylation profiles of genes utilizing newly developed CpG island methylation microarray on colorec - http://nar.oxfordjournals.org/cgi/content/full/33/5/e46

Category: DNA Microarray Protocols: DNA Methylation Microarray CpG

Kimura et al., NAR 2005. "easy-handling technology provided reproducible and precise measurement of methylated CpGs in MGMT promoter and, thus, our method may bring about a potential evolution in the handling of a variety of high-throughput DNA methylatio - [Read Methylation profiles of genes utilizing newly developed CpG island methylation microarray on colorec]

Methylation Specific PCR Protocol - http://www.mdanderson.org/departments/methylation/display.cfm?id=0CB11381-59AE-4D90-AC0B343F2D646EDD&method=displayFull&pn=A3F15D82-C9B4-41CD-BA4BE767E50A73D2

Category: Epigenetics and Methylation Protocols

Methylation Specific PCR Protocol. M.D Anderson Cancer Centre Texas. Protocol written by James Herman* - [Read Methylation Specific PCR Protocol]

Methylation-Specific Digital Karyotyping Protocol - http://www.natureprotocols.com/2006/11/09/methylationspecific_digital_ka.php

Category: Cytogenetics Protocols

Protocol describes a recently developed method — methylation-specific digital karyotyping (MSDK) — that enables comprehensive and unbiased genome-wide DNA methylation analysis. Using a combination of a methylation-sensitive mapping enzyme (for example, AscI) and a fragmenting enzyme (for example, NlaIII), short sequence tags can be obtained and uniquely mapped to genome location. - [Read Methylation-Specific Digital Karyotyping Protocol]

Methylation-Specific PCR Protocol - http://www.mdanderson.org/departments/methylation/display.cfm?id=0CB11381-59AE-4D90-AC0B343F2D646EDD&method=displayFull&pn=A3F15D82-C9B4-41CD-BA4BE767E50A73D2

Category: Nucleic Acid Modification Protocols: DNA Methylation Protocols

Protocol for methylation-specific PCR. - [Read Methylation-Specific PCR Protocol]

Monosaccharide Analysis of Phosphorylated Sugars by Methanolysis and Diazomethane Methylation - http://www.cshprotocols.org/cgi/content/extract/2006/1/pdb.prot4248

Category: Chromatography Protocols: Gas Chromatography Protocols

Protocol presents a method that allows rapid determination of the monosaccharide composition of glycans, glycoproteins, and proteoglycans that contain (or are suspected to contain) phosphorylated sugars. (For samples that do not contain phosphorylated sugars see Monosaccharide Analysis by Methanolysis.) - [Read Monosaccharide Analysis of Phosphorylated Sugars by Methanolysis and Diazomethane Methylation]

Quantification of DNA Methylation in Electrofluidics Chips Protocol - http://www.natureprotocols.com/2006/06/23/quantification_of_dna_methylat.php

Category: Nucleic Acid Modification Protocols: DNA Methylation Protocols

Protocol for quantification of DNA methylation in electrofluidics chips. Describe Bio-COBRA, a modified protocol for Combined Bisulfite Restriction Analysis (COBRA), that incorporates an electrophoresis step in microfluidics chips. Microfluidics technology involves the handling of small amounts of liquid in miniaturized systems. - [Read Quantification of DNA Methylation in Electrofluidics Chips Protocol]

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