Protocols: table of contents
| Authors | Protocol title | Category | Reviewers |
|---|---|---|---|
| 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 |
| 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 |
| Preparation of extended chromatin fibers from human tissue culture cells (Prot 55) | Fluorescence Microscopy | David Tremethick | |
| The MultiBac BEVS for producing proteins and their complexes (prot 54) | Complex Purification/Proteomics | Anika Altenfeld and Andrea Musacchio | |
| LNA containing probe synthesis (Prot 53) | Chromatin Biochemistry | Jose Antao | |
| Proteomics of isolated chromatin segments (PICh) on human telomeres (Prot 52) | Chromatin Biochemistry | Jose Antao | |
| 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) | – |
| 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 |
| Basic Analysis of NimbleGen ChIP-on-chip Data using Bioconductor/R (Prot 43) | Bioinformatics | Fabio Mohn, Tim Roloff | |
| 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 |
| 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 |
| 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) | – |
| 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 |
| Chromatin immunoprecipitation on native chromatin from cells and tissues (Prot 22) | Chromatin immunoprecipitation (ChIP) | Annabelle Lewis | |
| Site-directed hydroxy radical mapping of nucleosome positions in vitro (Prot 21) | Chromatin Biochemistry | Jeff Hayes | |
| Linear amplification of limiting amounts of RNA for gene expression studies (Prot 20) | RNA Analysis | Edward Oakley | |
| Tracking individual chromosomes with integrated arrays of Lacop sites and GFP-Laci repressor (Prot 15) | Chromosome Conformation | Julio Vazquez | |
| Plant DNA methylation analysis by “bisulfite genomic sequencing” (Prot 14) | DNA Methylation | Ales Kovarik | |
| Chromatin Immunoprecipitation Protocol to Analyze Histone Modifications in Arabidopsis thaliana (Prot 12) | Chromatin immunoprecipitation (ChIP) | Olivier Mathieu | |
| Chromatin Immunoprecipitation (ChIP) Assay (Prot 11) | Chromatin immunoprecipitation (ChIP) | Sergei Denisov, Arjen Brinkmann | |
| RNAse A Treatment of Mouse Cells (Prot 10) | RNA Analysis | Alessia Buscaino | |
| TSA Treatment of Mammalian Cells (Prot 9) | Histone Modifications/Antibodies | Bryan Turner | |
| 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 |
| RNA FISH on cultured cells in interphase (Prot 6) | Fluorescence Microscopy | Edith Heard | |
| Peter Fraser | Chromosome Conformation Capture (3C) (Prot 5) | Chromosome Conformation | Job Dekker |
| Giacomo Cavalli | Fluorescent in situ Hybridization Combined with Immunostaining on Polytene Chromosomes (Prot 4) | Fluorescence Microscopy | Sergio Pimpinelli, Laura Fanti |
| Chromatin Immunoprecipitation Protocol for Histone Modification & Chromatin Associated Proteins (Prot 3) | Chromatin immunoprecipitation (ChIP) | Antigone Kouskouti, Irene Kyrmizi | |
| Competing Chromosomal Proteins from Drosophila Polytene Chromosomes Using Modified Histone Peptides (Prot 2) | Fluorescence Microscopy | – | |
| Preparation and Immunostaining of Polytene Chromosome Squashes (Prot 1) | Fluorescence Microscopy | Cristina Chioda |
