Saturday, January 27, 2018

DNA Modification/Epigenetics

Analysis of Mitotic Checkpoint Function in Xenopus Egg Extracts
Yinghui Mao
Cold Spring Harb Protoc 2018; doi:10.1101/pdb.prot099853

Analysis of DNA Methylation in Mammalian Cells
Paul M. Lizardi, Qin Yan, and Narendra Wajapeyee
Cold Spring Harb Protoc 2017; doi:10.1101/pdb.top094821

Methylation-Specific Polymerase Chain Reaction (PCR) for Gene-Specific DNA Methylation Detection Paul M. Lizardi, Qin Yan, and Narendra Wajapeyee
Cold Spring Harb Protoc 2017; doi:10.1101/pdb.prot094847

Methyl-Cytosine-Based Immunoprecipitation for DNA Methylation Analysis
Paul M. Lizardi, Qin Yan, and Narendra Wajapeyee
Cold Spring Harb Protoc 2017; doi:10.1101/pdb.prot094854

High-Throughput Deep Sequencing for Mapping Mammalian DNA Methylation
Paul M. Lizardi, Qin Yan, and Narendra Wajapeyee
Cold Spring Harb Protoc 2017; doi:10.1101/pdb.prot094862

DNA Bisulfite Sequencing for Single-Nucleotide-Resolution DNA Methylation Detection
Paul M. Lizardi, Qin Yan, and Narendra Wajapeyee
Cold Spring Harb Protoc 2017; doi:10.1101/pdb.prot094839

Illumina Sequencing of Bisulfite-Converted DNA Libraries
Paul M. Lizardi, Qin Yan, and Narendra Wajapeyee
Cold Spring Harb Protoc 2017; doi:10.1101/pdb.prot094870

Micrococcal Nuclease Digestion of Schizosaccharomyces pombe Chromatin
Hugh P. Cam and Simon Whitehall
Cold Spring Harb Protoc 2016; doi:10.1101/pdb.prot091538

Oncogenomics Methods and Resources
Simon J. Furney, Gunes Gundem, and Nuria Lopez-Bigas
Cold Spring Harb Protoc 2012; doi:10.1101/pdb.top069229

Detection of Cytosine Methylation in RNA Using Bisulfite Sequencing
Tim Pollex, Katharina Hanna, and Matthias Schaefer
Cold Spring Harb Protoc 2010; doi:10.1101/pdb.prot5505

In Vitro Histone Demethylase Assay
Yu-ichi Tsukada and Keiichi I. Nakayama
Cold Spring Harb Protoc 2010; doi:10.1101/pdb.prot5512

Potassium Permanganate Probing of Pol II Open Complexes
Michael F. Carey, Craig L. Peterson, and Stephen T. Smale
Cold Spring Harb Protoc 2010; doi:10.1101/pdb.prot5479

Amplification of Bisulfite-Converted DNA for Genome-Wide DNA Methylation Profiling Jon Reinders
Cold Spring Harb Protoc 2009; doi:10.1101/pdb.prot5342

In Vivo DNase I, MNase, and Restriction Enzyme Footprinting via Ligation-Mediated Polymerase Chain Reaction (LM-PCR)
Michael F. Carey, Craig L. Peterson, and Stephen T. Smale
Cold Spring Harb Protoc 2009; doi:10.1101/pdb.prot5277

In Vivo Dimethyl Sulfate (DMS) Footprinting via Ligation-Mediated Polymerase Chain Reaction (LM-PCR) Michael F. Carey, Craig L. Peterson, and Stephen T. Smale
Cold Spring Harb Protoc 2009; doi:10.1101/pdb.prot5278

Chromatin Immunoprecipitation (ChIP)
Michael F. Carey, Craig L. Peterson, and Stephen T. Smale
Cold Spring Harb Protoc 2009; doi:10.1101/pdb.prot5279

Native Chromatin Preparation and Illumina/Solexa Library Construction
Suresh Cuddapah, Artem Barski, Kairong Cui, Dustin E. Schones, Zhibin Wang, Gang Wei, and Keji Zhao
Cold Spring Harb Protoc 2009; doi:10.1101/pdb.prot5237

Reconstitution of Nucleosomal Arrays Using Recombinant Drosophila ACF and NAP1Craig L. Peterson
Cold Spring Harb Protoc 2009; doi:10.1101/pdb.prot5114

Purification of Recombinant Drosophila ACF
Craig L. Peterson
Cold Spring Harb Protoc 2009; doi:10.1101/pdb.prot5115

Purification of Recombinant Drosophila NAP1
Craig L. Peterson
Cold Spring Harb Protoc 2009; doi:10.1101/pdb.prot5116

Combined 3C-ChIP-Cloning (6C) Assay: A Tool to Unravel Protein-Mediated Genome Architecture
Vijay K. Tiwari and Stephen B. Baylin
Cold Spring Harb Protoc 2009; doi:10.1101/pdb.prot5168

Chromosome Conformation Capture
Nathan F. Cope and Peter Fraser
Cold Spring Harb Protoc 2009; doi:10.1101/pdb.prot5137

Chicken Erythrocyte Histone Octamer Preparation
Craig L. Peterson and Jeffrey C. Hansen
Cold Spring Harb Protoc 2008; doi:10.1101/pdb.prot5112

Salt Gradient Dialysis Reconstitution of Nucleosomes
Craig L. Peterson
Cold Spring Harb Protoc 2008; doi:10.1101/pdb.prot5113

DNA Methylation Analysis of Human Imprinted Loci by Bisulfite Genomic Sequencing
Vanessa T. Angeles and Renee A. Reijo Pera
Cold Spring Harb Protoc 2008; doi:10.1101/pdb.prot5046

Coimmunoprecipitation (co-IP) of Nuclear Proteins and Chromatin Immunoprecipitation (ChIP) from Arabidopsis
Berthe Katrine Fiil, Jin-Long Qiu, Klaus Petersen, Morten Petersen, and John Mundy
Cold Spring Harb Protoc 2008; doi:10.1101/pdb.prot5049

Mapping Protein Distributions on Polytene Chromosomes by Immunostaining
Renato Paro
Cold Spring Harb Protoc 2008; doi:10.1101/pdb.prot4714

DNA Immunoprecipitation (DIP) for the Determination of DNA-Binding Specificity
Andrea J. Gossett and Jason D. Lieb
Cold Spring Harb Protoc 2008; doi:10.1101/pdb.prot4972

Methylated CpG Island Amplification and Microarray (MCAM) for High-Throughput Analysis of DNA Methylation
Marcos R. H. Estécio, Pearlly S. Yan, Tim H-M. Huang, and Jean-Pierre J. Issa
Cold Spring Harb Protoc 2008; doi:10.1101/pdb.prot4974

In Vitro Histone Methyltransferase Assay
Ian M. Fingerman, Hai-Ning Du, and Scott D. Briggs
Cold Spring Harb Protoc 2008; doi:10.1101/pdb.prot4939

Development of Mammalian Cell Lines with lac Operator-Tagged Chromosomes
Yuri G. Strukov and Andrew S. Belmont
Cold Spring Harb Protoc 2008; doi:10.1101/pdb.prot4903

Micrococcal Nuclease-Southern Blot Assay: I. MNase and Restriction Digestions
Michael Carey and Stephen T. Smale
Cold Spring Harb Protoc 2007; doi:10.1101/pdb.prot4890

Micrococcal Nuclease-Southern Blot Assay: II. Capillary Transfer and Hybridization
Michael Carey and Stephen T. Smale
Cold Spring Harb Protoc 2007; doi:10.1101/pdb.prot4891

Chromatin Immunoprecipitation (ChIP) on Unfixed Chromatin from Cells and Tissues to Analyze Histone Modifications
Alexandre Wagschal, Katia Delaval, Maëlle Pannetier, Philippe Arnaud, and Robert Feil
Cold Spring Harb Protoc 2007; doi:10.1101/pdb.prot4767

PCR-Based Analysis of Immunoprecipitated Chromatin
Alexandre Wagschal, Katia Delaval, Maëlle Pannetier, Philippe Arnaud, and Robert Feil
Cold Spring Harb Protoc 2007; doi:10.1101/pdb.prot4768

Yeast Chromatin Immunoprecipitation (ChIP) Assay
William P. Tansey
Cold Spring Harb Protoc 2007; doi:10.1101/pdb.prot4642

Denaturing Protein Immunoprecipitation from Yeast
William P. Tansey
Cold Spring Harb Protoc 2007; doi:10.1101/pdb.prot4643

Chromatin Immunoprecipitation (ChIP) of Protein Complexes: Mapping of Genomic Targets of Nuclear Proteins in Cultured Cells
Achim Breilingand Valerio Orlando
Cold Spring Harb Protoc 2006; doi:10.1101/pdb.prot4560

Mapping DNase-I-hypersensitive Sites
Joseph Sambrook and David W. Russell
Cold Spring Harb Protoc 2006; doi:10.1101/pdb.prot3949

Chromatin Immunoprecipitation in Yeast
David C. Amberg, Daniel J. Burke, and Jeffrey N. Strathern
Cold Spring Harb Protoc 2006; doi:10.1101/pdb.prot4177


No comments: