Advancing Epigenetics Towards Systems Biology

Protocols: table of contents

AuthorsProtocol titleCategoryReviewers
Isabel Chillón, Marco Marcia, Michal Legiewicz, Fei Liu, Srinivas Somarowthu and Anna Marie Pyle Native Purification and Analysis of Long RNAs (Prot 71) RNA Analysis -
Ambre Bender, Michael Weber Preparation of Reduced Representation Bisulfite Sequencing (RRBS) libraries (Prot 70) DNA Methylation -
Georg Kustatscher, Karen L. H. Wills, Cristina Furlan, Juri Rappsilber Chromatin Enrichment for proteomics (ChEP), (Prot 69) Complex Purification/Proteomics -
Pedro Madrigal Identification of Transcription Factor Binding Sites in ChIP-exo using R/Bioconductor (Prot 68) Bioinformatics Gordon Brown
Nicolas Delhomme, Niklas Mähler, Bastian Schiffthaler, David Sundell, Chanaka Mannapperuma, Torgeir R. Hvidsten, Nathaniel R. Street Guidelines for RNA-Seq data analysis (Prot 67) Bioinformatics Michael Love
Aurélien A. Sérandour, Jason S. Carroll ChIP-exonuclease in mammalian cells (Prot 66) Chromatin-Immunoprecipitation (ChIP) David J. Steger
Vuthy Ea, Thierry Forné, Franck Court Quantitative Chromosome Conformation Capture (3C-qPCR) (Prot 65) Chromosome Conformation -
 Elise Mahé, Gilles Salbert Hydroxymethylated DNA Immunoprecipitation (hMeDIP) in mammalian cells (Prot 64) Chromatin-Immunoprecipitation (ChIP) -
Alfredo Castello, Rastislav Horos, Claudia Strein, Bernd Fischer, Katrin Eichelbaum, Lars M. Steinmetz, Jeroen Krijgsveld, Matthias W. Hentze System-wide identification of RNA-binding proteins by interactome capture (Prot 63) RNA Analysis -
Elphège P. Nora, Edith Heard Engineering genomic deletions and inversions in mouse ES cells using custom designed nucleases (Prot 62) Genome engineering Claire Rougeulle
Arne H. Smits, Michiel Vermeulen Stoichiometry determination of protein complexes by label-free quantitative mass spectrometry-based proteomics (Prot 61) Complex Purification/Proteomics Angus Lamond
Tom Sexton, Sreenivasulu Kurukuti, Jennifer A Mitchell, David Umlauf, Takashi Nagano & Peter Fraser Sensitive detection of chromatin co-associations using enhanced chromosome conformation capture on chip (Prot 60) Chromosome Conformation -
Leif C. Lindeman, Philippe Collas Chromatin Immunoprecipitation Assay for Early Zebrafish Embryos (Prot 59) Chromatin-Immunoprecipitation (ChIP) Ferenc Müller
Oluwatosin Taiwo, Gareth A Wilsona, Tiffany Morris, Stefanie Seisenberger, Wolf Reik, Daniel Pearce, Stephan Beck, & Lee M Butcher Nano-MeDIP-seq: Methylome analysis using low DNA concentrations (Prot 58) DNA Methylation Jonathan Mill
Felix Krueger, Simon R Andrews Quality Control, trimming and alignment of Bisulfite-Seq data (Prot 57) Bioinformatics Christian Rohde
Ruhi Ali, Florence M.G. Cavalli, Juan M. Vaquerizas, Nicholas M. Luscombe A pipeline for ChIP-seq data analysis (Prot 56) Bioinformatics Gareth A Wilson
Elaine Dunleavy Preparation of extended chromatin fibers from human tissue culture cells (Prot 55) Fluorescence Microscopy David Tremethick
Frederic Garzoni, Christoph Bieniossek, Imre Berger The MultiBac BEVS for producing proteins and their complexes (prot 54)

Complex Purification/Proteomics

Anika Altenfeld and Andrea Musacchio
Elodie Rey, Jérôme Déjardin LNA containing probe synthesis (Prot 53) Chromatin Biochemistry Jose Antao
Paulina Marzec, Jérôme Déjardin Proteomics of isolated chromatin segments (PICh) on human telomeres (Prot 52)

Chromatin Biochemistry

Jose Antao
Ignasi Forné, Teresa Barth and Axel Imhof Quantifying histone modifications using mass spectrometry (Prot 51) Histone Modifications/Antibodies Stefan Kubicek
Julie K. Stock, Emily Brookes, Ana Pombo Phospho-sensitive chromatin immunoprecipitation of RNA Polymerase II (Prot 48) Chromatin-Immunoprecipitation (ChIP)  -
Matthias Siebert, Michael Lidschreiber, Holger Hartmann, and Johannes Söding A Guideline for ChIP - Chip Data Quality Control and Normalization (Prot 47) Bioinformatics Tobias Straub, Adolf-Butenandt
Andrew K. Roos, and Joanna Wysocka Peptide Pull-Down (PPD) Assay for Identification and Characterization of Histone PTM Effectors (Prot 46) Complex Purification/Proteomics Sandra Hake, Adolf‐Butenandt
Santhi Pondugula, Vamsi K. Gangaraju, Blaine Bartholomew, and Michael P.Kladde DNA methyltransferase-based single-molecule (MAPit) assay for mapping protein-DNA interactions in vitro (Prot 45) Chromatin Biochemistry  -
Karin Fellinger & Ulrich Rothbauer Quantitative immunoprecipitation of GFP-fusion proteins using the GFP-Trap (Prot 44) Complex purification/Proteomics Raffaella Villa
Tobias Straub Basic Analysis of NimbleGen ChIP-on-chip Data using Bioconductor/R (Prot 43) Bioinformatics Fabio Mohn, Tim Roloff
Andrew Routh, and Daniela Rhodes In vitro reconstitution of nucleosome arrays with a stoichiometric content of histone octamer and linker histone (Prot 42) Chromatin Biochemistry Verena Maier
Zuzana Jasencakova and Anja Groth Purification of Human Multiprotein Complexes using OneSTrEP Technology (Prot 41) Complex purification/Proteomics Adam Cook
Ericka Havecker Cloning of small RNAs with 5' phosphate and 3' OH ends (Prot 40) RNA analysis Eric Miska
Takumi Takizawa and Tom Misteli Sequential RNA and DNA fluorescence in situ hybridization (Prot 39) Fluorescence Microscopy Lyubomira Chakalova, Peter Fraser
Tina B. Miranda, Einav Gal-Yam, Gerda Egger, Joy Lin, Shinwu Jeong, and Peter A. Methyltransferase-based single-promoter analysis assay (Prot 38) DNA Methylation Michael P. Kladde
Petr Svoboda Petr Svoboda Bisulfite sequencing of very small samples (Prot 37) DNA Methylation Jörn E. Walter
Ana María Poveda Gabaldón, Hélène Tourrière, Constance Alabert and Philippe Pasero Single-molecule analysis of DNA replication by molecular combing (Prot 36) Single Molecule Nick Rhind
Sascha Tierling, Sabine Reither, Jörn Walt Bisulfite sequencing of small DNA/cell samples (Prot 35) DNA Methylation Jörg Tost
Agustin Fernandez-Fernandez & Manel Esteller DNA Methylation Analysis by Bisulfite Sequencing (Prot 34) DNA Methylation Jörn Walter
Michaël Weber and Dirk Schübeler Methylated DNA Immunoprecipitation (MeDIP) (Prot 33) DNA Methylation  -
Kevin V. Morris RNA-biotin based pulldown assays for the detection of siRNA targeted genomic regions and siRNA directed histone modifications (Prot 32) RNA Analysis Jeannie Lee
Alice Horton, Tom Sexton and Peter Fraser Chromosome Conformation Capture (3C) (alternate technique) (Prot 31) Chromosome Conformation  -
Henriette O'Geen and Peggy Farnham Whole genome amplification protocol for ChIP-chip (Prot 30) Chromatin immunoprecipitation (ChIP) Angelika Mitterweger

Antonio Porro and Giovanni Perini

In vivo dual cross-linking chromatin immunoprecipitation: detecting chromatin proteins not directly bound to DNA (Prot 29) Chromatin immunoprecipitation (ChIP) Bernd Schuettengruber
Bryan K. Sun & Jeannie T. Lee RNA-chromatin immunoprecipitations (RNA-ChIP) in mammalian cells (Prot 28) RNA Analysis Kevin V. Morris
Roderick O'Sullivan & Joost Martens Chromatin immunoprecipitation protocol for Saccharomyces cerevisiae (Prot 27) Chromatin immunoprecipitation (ChIP) Xuetong (Snow) Shen
Laura O'Neill & Bryan Turner Carrier ChIP (CChIP) (Prot 26) Chromatin immunoprecipitation (ChIP) -
Patrick Heun Live imaging with Drosophila tissue culture cells (Prot 25) Fluorescence Microscopy Helder Maiato
 Marion Cremer, Claudia Weierich & Irina Solovei Multicolour 3D-FISH in vertebrate cells (Prot 23) Fluorescence Microscopy Luis Antonio Parada
David Umlauf, Yuji Goto, Katia Delaval, Alexandre Wagschal, Philippe Arnaud & Robert Feil Chromatin immunoprecipitation on native chromatin from cells and tissues (Prot 22) Chromatin immunoprecipitation (ChIP) Annabelle Lewis
Andrew Flaus, Chris Stockdale, Elisa Garcia-Wilson, Maik Engeholm, Helder Ferreira, & Tom Owen-Hughes Site-directed hydroxy radical mapping of nucleosome positions in vitro (Prot 21) Chromatin Biochemistry Jeff Hayes
Alexandra Schebesta & Shane McManus Linear amplification of limiting amounts of RNA for gene expression studies (Prot 20) RNA Analysis Edward Oakley
Frank Neumann, Angela Taddei & Susan Gasser Tracking individual chromosomes with integrated arrays of Lacop sites and GFP-Laci repressor (Prot 15) Chromosome Conformation Julio Vazquez
Michael Mette Plant DNA methylation analysis by "bisulfite genomic sequencing" (Prot 14) DNA Methylation Ales Kovarik
Werner Aufsatz Chromatin Immunoprecipitation Protocol to Analyze Histone Modifications in Arabidopsis thaliana (Prot 12) Chromatin immunoprecipitation (ChIP) Olivier Mathieu
Antigone Kouskouti & Irene Kyrmizi Chromatin Immunoprecipitation (ChIP) Assay (Prot 11) Chromatin immunoprecipitation (ChIP) Sergei Denisov, Arjen Brinkmann
Christèle Maison RNAse A Treatment of Mouse Cells (Prot 10) RNA Analysis Alessia Buscaino
Daniéle Roche TSA Treatment of Mammalian Cells (Prot 9) Histone Modifications/Antibodies Bryan Turner
Chaumeil J., Chow J., Augui S., Edith Heard Immunofluorescence and Fluorescent In Situ Hybridization in Mouse Fibroblasts and Embryonic Stem Cells (Prot 8) Fluorescence Microscopy Joost Gribnau
Frédéric Bantignies, Charlotte Grimaud & Giacomo Cavalli Two-colour fluorescent in situ DNA hybridization on whole mount Drosophila embryos and larval imaginal discs (Prot 7) Fluorescence Microscopy Cornelia Fritsch, Donna Arndt-Jovin
Karen Ng RNA FISH on cultured cells in interphase (Prot 6) Fluorescence Microscopy Edith Heard
Alice Horton & Peter Fraser Chromosome Conformation Capture (3C) (Prot 5) Chromosome Conformation Job Dekker
Charlotte Grimaud, Frédéric Bantignies & Giacomo Cavalli Fluorescent in situ Hybridization Combined with Immunostaining on Polytene Chromosomes (Prot 4) Fluorescence Microscopy Sergio Pimpinelli, Laura Fanti
Roderick O'Sullivan & Joost Martens Chromatin Immunoprecipitation Protocol for Histone Modification & Chromatin Associated Proteins (Prot 3) Chromatin immunoprecipitation (ChIP) Antigone Kouskouti, Irene Kyrmizi
Leonie Ringrose Competing Chromosomal Proteins from Drosophila Polytene Chromosomes Using Modified Histone Peptides (Prot 2) Fluorescence Microscopy  -
Christine James, Paul Badenhorst & Bryan Turner Preparation and Immunostaining of Polytene Chromosome Squashes (Prot 1) Fluorescence Microscopy Cristina Chioda