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
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