| 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 |
