Cold Spring Harbor Laboratory Protocols

The following Cold Spring Harbor Laboratory Press protocols are brought to you by BioSupplyNet in a partnership with Sigma-Aldrich. A list of products is available to use in each protocol.

Protocols available for:

• Antibodies
• RNAi
• Genomics
• Neuroscience
• Proteomics
• Stem Cell Biology

Antibodies

Removal of Cross-reactive Antibodies from Antiserum: Affinity Chromatography For a product list of materials for this protocol, click here. Histological Preparation of Embryonic and Adult Zebrafish Eyes For a product list of materials for this protocol, click here. Nondenaturing Protein Immunoprecipitation from Mammalian Cells For a product list of materials for this protocol, click here. Yeast Chromatin Immunoprecipitation (ChIP) Assay For a product list of materials for this protocol, click here.

Selected Protocols from "Using Antibodies," Ed Harlow and David Lane. Epitope Mapping by Competition Assay For a product list of materials for this protocol, click here.

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RNAi

Selected Protocols from "Manipulating the Mouse Embryo," 3rd Edition, Andras Nagy et al. Culturing Trophoblast Stem (TS) Cell Lines For a product list of materials for this protocol, click here. In Situ Hybridization of Whole-Mount Mouse Embryos with RNA Probes: Hybridization, Washes, and Histochemistry For a product list of materials for this protocol, click here. Production of Endoribonuclease-Prepared Short Interfering RNAs (esiRNAs) for Specific and Effective Gene Silencing in Mammalian Cells For a product list of materials for this protocol, click here.

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Selected Protocols from "RNAi, A Guide to Gene Silencing," Gregory J. Hannon. Mammalian RNA Interference, Thomas Tuschl (Chapter 13, pg. 280-288) Production of dsRNA for RNAi in Avian Embryos For a product list of materials for this protocol, click here. Microinjection of dsRNA into Mouse Oocytes and Early Embryos For a product list of materials for this protocol, click here. Selection of siRNA Sequences For a product list of materials for this protocol, click here. Annealing siRNAs to Produce siRNA Duplexes For a product list of materials for this protocol, click here. Cell Culture and Preparation of Cells in 24-Well Plates For a product list of materials for this protocol, click here. Cotransfection of Luciferase Reporter Plasmids with siRNA Duplexes For a product list of materials for this protocol, click here. Transfection of siRNA Duplexes For a product list of materials for this protocol, click here. Immunofluorescence Detection of Protein Knockdown For a product list of materials for this protocol, click here. Detection of Protein Knockdown by Western Blotting For a product list of materials for this protocol, click here.

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Selected Protocols from "Gene Transfer: Delivery and Expression of DNA and RNA," by Theodore Friedmann and John Rossi. Genetic Manipulation of Mammalian Cells by Microinjection For a product list of materials for this protocol, click here. Knockdown Transgenic Mice Generated by Silencing Lentiviral Vectors For a product list of materials for this protocol, click here. Lentivirus Transduction of Hematopoietic Cells For a product list of materials for this protocol, click here.

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Genomics

Selected Protocols from "Gene Transfer: Delivery and Expression of DNA and RNA," by Theodore Friedmann and John Rossi. Preparation of Biodegradable Nanoparticles and Their Use in Transfection For a product list of materials for this protocol, click here. Genome Modification by Inclusion of loxP Transgene Sequences For a product list of materials for this protocol, click here. Fate-Mapping Technique: Targeted Whole-Embryo Electroporation of DNA Constructs into the Germ Layers of Mouse Embryos 7–7.5 Days Post-coitum For a product list of materials for this protocol, click here. Generation of Transgenic Xenopus laevis For a product list of materials for this protocol, click here. Genotyping by Oligonucleotide Ligation Assay (OLA) For a product list of materials for this protocol, click here. Chromatin Immunoprecipitation (ChIP) on Unfixed Chromatin from Cells and Tissues to Analyze Histone Modifications For a product list of materials for this protocol, click here. PCR-Based Analysis of Immunoprecipitated Chromatin For a product list of materials for this protocol, click here.

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Selected Protocols from "Molecular Cloning: A Laboratory Manual, 3rd ed., Vols 1, 2, and 3," Joe Sambrook and David Russell. Purification of PCR Products in Preparation for Cloning For a product list of materials for this protocol, click here. Selection of Poly(A)+ RNA by Oligo(dT)-Cellulose Chromatography For a product list of materials for this protocol, click here. Isolation of BAC DNA from Large-scale Cultures For a product list of materials for this protocol, click here. Quantitative PCR For a product list of materials for this protocol, click here. The Inoue Method for Preparation and Transformation of Competent E. coli: "Ultra Competent" Cells For a product list of materials for this protocol, click here. Preparation of Plasmid DNA by Alkaline Lysis with SDS: Maxipreparation For a product list of materials for this protocol, click here. Removal of Ethidium Bromide from DNA by Extraction with Organic Solvents For a product list of materials for this protocol, click here.

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Neuroscience

PEI Nanoparticles for Targeted Gene Delivery For a product list of materials for this protocol, click here.

Selected Protocols from "Transfecting Cultured Hippocampal Neurons with an Actin-GFP Plasmid," D. Spector & R. Goldman. Transfecting Cultured Hippocampal Neurons with an Actin-GFP Plasmid For a product list of materials for this protocol, click here.

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Proteomics

Selected Protocols from "Protein-Protein Interactions," 2nd Edition, E. Golemis, P. Adam. Protein Interactions Captured by Chemical Cross-linking: One-Step Cross-linking with Formaldehyde For a product list of materials for this protocol, click here. cAMP Assays For a product list of materials for this protocol, click here. Using Genetically Engineered Kinases to Screen for Novel Protein Kinase Substrates For a product list of materials for this protocol, click here. Purification of Expressed Proteins from Inclusion Bodies For a product list of materials for this protocol, click here. Phosphorylation of Substrates For a product list of materials for this protocol, click here. Identification of a Mutant Kinase/ATP Analog Pair For a product list of materials for this protocol, click here. Preparation of Glutathione-S-Transferase (GST) Fusion Proteins For a product list of materials for this protocol, click here. Synthesis and Probing of Membrane-bound Peptide Arrays For a product list of materials for this protocol, click here. Fine Mapping of Genomic Targets of Nuclear Proteins in Cultured Cells For a product list of materials for this protocol, click here. Screening Kinase Phosphorylation Motifs Using Peptide Libraries For a product list of materials for this protocol, click here. Digestion of Proteins and Extraction of Peptides from an Acrylamide Gel For a product list of materials for this protocol, click here. Direct Enzymatic Digestion of Protein Complexes For a product list of materials for this protocol, click here.

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Selected Protocol from "Proteins and Proteomics: A Laboratory Manual," Richard J. Simpson. Preparation of Reversed-Phase Microcolumns For a product list of materials for this protocol, click here. Characterization of Phosphopeptides Using a Combination of Immobilized Metal Ion Affinity Media and Direct Analysis by MALDI-TOF-MS For a product list of materials for this protocol, click here. Analysis of the Topology of Protein Complexes Using Cross-Linking and Mass Spectrometry For a product list of materials for this protocol, click here. Preparation and Use of an Integrated Microcapillary HPLC Column and ESI Device for Proteomic Analysis For a product list of materials for this protocol, click here. Analysis of Complex Protein Mixtures Using Multidimensional Protein Identification Technology (MuDPIT) For a product list of materials for this protocol, click here. General Method for MALDI-MS Analysis of Proteins and Peptides For a product list of materials for this protocol, click here. Isotope-coded Affinity Tagging of Proteins For a product list of materials for this protocol, click here. In Vivo Isotopic Labeling of Proteins for Quantitative Proteomics For a product list of materials for this protocol, click here.

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Stem Cell Biology

Culturing Trophoblast Stem (TS) Cell Lines For a product list of materials for this protocol, click here. Preparation of Biodegradable Nanoparticles and Their Use in Transfection For a product list of materials for this protocol, click here. In Situ Hybridization of Whole-Mount Mouse Embryos with RNA Probes: Hybridization, Washes, and Histochemistry For a product list of materials for this protocol, click here.

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