CSH Protocols, Free Featured Protocols

Current Issue

As samples of our content, Cold Spring Harbor Protocols is pleased to offer the following protocols for free access:

[DNase-seq: A High-Resolution Technique for Mapping Active Gene Regulatory Elements across the Genome from Mammalian Cells]

[Genome-Wide Analysis of DNA Synthesis by BrdU Immunoprecipitation on Tiling Microarrays (BrdU-IP-chip) in Saccharomyces cerevisiae]

Subject Categories

Antibodies
Bioinformatics/Genomics
Cell Biology
Developmental Biology
DNA Delivery/Gene Transfer
Genetics
High-Throughput Analysis
Imaging/Microscopy
Immunology
Laboratory Organisms
Molecular Biology
Neuroscience
Plant Biology
Polymerase Chain Reaction (PCR)
Proteins and Proteomics
RNA Interference (RNAi)/siRNA
Stem Cells
Transgenic Technology

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Antibodies

[Analysis of RNA-Protein Complexes by RNA Coimmunoprecipitation and RT-PCR Analysis from Caenorhabditis elegans]

[Chromatin Immunoprecipitation (ChIP)]

[Chromatin Immunoprecipitation (ChIP) of Protein Complexes: Mapping of Genomic Targets of Nuclear Proteins in Cultured Cells]

[Chromatin Immunopreciptation (ChIP) on Unfixed Chromatin from Cells and Tissues to Analyze Histone Modifications]

[Combined 3C-ChIP-Cloning (6C) Assay: A Tool to Unravel Protein-Mediated Genome Architecture]

[Combined Flow Cytometric Measurement of Two Cell-Surface Antigens and DNA-RNA Content]

[DNA Immunoprecipitation (DIP) for the Determination of DNA-Binding Specificity]

[Dual-Color ELISPOT Assay for the Simultaneous Detection of IL-2 and IFN-γ Secreting T Cells]

[Mapping Protein Distributions on Polytene Chromosomes by Immunostaining]

[Native Chromatin Preparation and Illumina/Solexa Library Construction]

Bioinformatics / Genomics

[Assays with Protein Arrays]

[Browsing HapMap Data Using the Genome Browser]

[Choosing a Method for Phylogenetic Prediction]

[Combined 3C-ChIP-Cloning (6C) Assay: A Tool to Unravel Protein-Mediated Genome Architecture]

[Copy Number Variation Detection via High-Density SNP Genotyping]

[Genotyping by Oligonucleotide Ligation Assay (OLA)]

[Laboratory Methods for High-Throughput Genotyping]

[Methylated CpG Island Amplification and Microarray (MCAM) for High-Throughput Analysis of DNA Methylation]

[Native Chromatin Preparation and Illumina/Solexa Library Construction]

[SNP Mining from Maize 454 EST Sequences]

[Using the Basic Local Alignment Search Tool (BLAST)]

Cell Biology

[A Sealed Preparation for Long-Term Observations of Cultured Cells]

[Adhesive Micropatterns for Cells: A Microcontact Printing Protocol]

[Bone Marrow-Derived Macrophages (BMM): Isolation and Applications]

[Chromatin Immunoprecipitation (ChIP)]

[Chromatin Immunoprecipitation (ChIP) of Protein Complexes: Mapping of Genomic Targets of Nuclear Proteins in Cultured Cells]

[Chromatin Immunopreciptation (ChIP) on Unfixed Chromatin from Cells and Tissues to Analyze Histone Modifications]

[Combined 3C-ChIP-Cloning (6C) Assay: A Tool to Unravel Protein-Mediated Genome Architecture]

[Combined Flow Cytometric Measurement of Two Cell-Surface Antigens and DNA-RNA Content]

[Cultures of Cerebellar Granule Neurons]

[Culturing Human Embryonic Stem Cells in Feeder-Free Conditions]

[Cutaneous Two-Stage Chemical Carcinogenesis]

[Design and Cloning of an shRNA into a Lentiviral Silencing Vector: Version A]

[Development of Mammalian Cell Lines with lac Operator-Tagged Chromosomes]

[Dual-Color ELISPOT Assay for the Simultaneous Detection of IL-2 and IFN-γ Secreting T Cells]

[Ex Ovo Electroporation of DNA Vectors into Pre-gastrulation Avian Embryos]

[Fate-Mapping Technique: Using Carbocyanine Dyes for Vital Labeling of Cells in Gastrula-Stage Mouse Embryos Cultured in Vitro]

[Fetal Thymus Organ Culture]

[Fluorescence In Situ Hybridization for the Identification of Environmental Microbes]

[Fluorescent Protein Tracking and Detection: Fluorescent Protein Structure and Color Variants]

[Hematopoietic Stem Cell Targeting with Surface-Engineered Lentiviral Vectors]

[Immunohistochemistry of Whole-Mount Mouse Embryos]

[In Vitro Assays for the Extracellular Matrix Protein-Regulated Extravasation Process]

[Isolation and Whole-Cell Patch Clamping of Arabidopsis Guard Cell Protoplasts]

[Isolation, Culture, and Differentiaton of Progenitor Cells from the Central Nervous System]

[Live-Cell Imaging of GFP in Plants]

[Live Imaging of Caenorhabditis elegans: Examples]

[Microinjection of Protein Samples]

[Noninvasive Human Nuclear Transfer with Embryonic Stem Cells]

[Photoactivation-Based Labeling and In Vivo Tracking of RNA Molecules in the Nucleus]

[Preparation of Complex DNA Probe Sets for 3D FISH with up to Six Different Fluorochromes]

[Preparation of Rodent Hippocampal Slice Cultures]

[Preparing Recombinant Gonad Organ Cultures]

[Production of Endoribonuclease-Prepared Short Interfering RNAs (esiRNAs) for Specific and Effective Gene Silencing in Mammalian Cells]

[Regulating Protein Stability in Mammalian Cells Using Small Molecules]

[Selection of Appropriate Imaging Equipment and Methodology for Live Cell Imaging in Drosophila]

[Staining Whole Mouse Embryos for β-Galactosidase (lacZ) Activity]

[Studying Mitosis in Cultured Mammalian Cells]

[The OP9-DL1 System: Generation of T-Lymphocytes from Embryonic or Hematopoietic Stem Cells In Vitro]

[Transcript In Situ Hybridization of Whole-Mount Embryos for Phenotype Analysis of RNAi-Treated Drosophila]

[Use of Fluorescence In Situ Hybridization and the daime Image Analysis Program for the Cultivation-Independent Quantification of Microorganisms in Environmental and Medical Samples]

[Whole-Mount In Situ Hybridization of RNA Probes to Plant Tissues]

[Xenopus laevis Keller Explants]

Developmental Biology

[Culturing Human Embryonic Stem Cells in Feeder-Free Conditions]

[Design and Cloning of an shRNA into a Lentiviral Silencing Vector: Version A]

[Ex Ovo Electroporation of DNA Vectors into Pre-gastrulation Avian Embryos]

[Fate-Mapping Technique: Using Carbocyanine Dyes for Vital Labeling of Cells in Gastrula-Stage Mouse Embryos Cultured in Vitro]

[Fetal Thymus Organ Culture]

[Immunohistochemistry of Whole-Mount Mouse Embryos]

[Injection of dsRNA into Drosophila Embryos for RNA Interference (RNAi)]

[Isolation, Culture, and Differentiaton of Progenitor Cells from the Central Nervous System]

[Microinjection of dsRNA into Mouse Oocytes and Early Embryos]

[Mouse Mutagenesis Using N-Ethyl-N-Nitrosourea (ENU)]

[Noninvasive Human Nuclear Transfer with Embryonic Stem Cells]

[Planarians: A Versatile and Powerful Model System for Molecular Studies of Regeneration, Adult Stem Cell Regulation, Aging, and Behavior]

[Preparing Recombinant Gonad Organ Cultures]

[Production of Endoribonuclease-Prepared Short Interfering RNAs (esiRNAs) for Specific and Effective Gene Silencing in Mammalian Cells]

[SIRT Combines Homologous Recombination, Site-Specific Integration, and Bacterial Recombineering for Targeted Mutagenesis in Drosophila]

[Staining Whole Mouse Embryos for β-Galactosidase (lacZ) Activity]

[The Genus Antirrhinum (Snapdragon): A Flowering Plant Model for Evolution and Development]

[Transcript In Situ Hybridization of Whole-Mount Embryos for Phenotype Analysis of RNAi-Treated Drosophila]

[Use of the Sleeping Beauty Transposon System for Stable Gene Expression in Mouse Embryonic Stem Cells]

[Virus-Induced Gene Silencing as a Tool for Delivery of dsRNA into Plants]

[Xenopus laevis Keller Explants]

DNA Delivery/Gene Transfer

[Construction and Characterization of Adenovirus Vectors]

[Construction of Gene-Targeting Vectors by Recombineering]

[Design and Cloning of an shRNA into a Lentiviral Silencing Vector: Version A]

[Development of Mammalian Cell Lines with lac Operator-Tagged Chromosomes]

[Ex Ovo Electroporation of DNA Vectors into Pre-gastrulation Avian Embryos]

[Hematopoietic Stem Cell Targeting with Surface-Engineered Lentiviral Vectors]

[Injection of dsRNA into Drosophila Embryos for RNA Interference (RNAi)]

[In Planta Transformation of Arabidopsis]

[Microinjection of dsRNA into Mouse Oocytes and Early Embryos]

[Regulating Protein Stability in Mammalian Cells Using Small Molecules]

[SIRT Combines Homologous Recombination, Site-Specific Integration, and Bacterial Recombineering for Targeted Mutagenesis in Drosophila]

[Use of the Sleeping Beauty Transposon System for Stable Gene Expression in Mouse Embryonic Stem Cells]

[Virus-Induced Gene Silencing as a Tool for Delivery of dsRNA into Plants]

Genetics

[Browsing HapMap Data Using the Genome Browser]

[Choosing a Method for Phylogenetic Prediction]

[Copy Number Variation Detection via High-Density SNP Genotyping]

[Genotyping by Oligonucleotide Ligation Assay (OLA)]

[Karyotyping Mouse Cells]

[Laboratory Methods for High-Throughput Genotyping]

[Mapping Protein Distributions on Polytene Chromosomes by Immunostaining]

[Methylated CpG Island Amplification and Microarray (MCAM) for High-Throughput Analysis of DNA Methylation]

[Mouse Mutagenesis Using N-Ethyl-N-Nitrosourea (ENU)]

[Production of Endoribonuclease-Prepared Short Interfering RNAs (esiRNAs) for Specific and Effective Gene Silencing in Mammalian Cells]

[SIRT Combines Homologous Recombination, Site-Specific Integration, and Bacterial Recombineering for Targeted Mutagenesis in Drosophila]

[SNP Mining from Maize 454 EST Sequences]

[Using the Basic Local Alignment Search Tool (BLAST)]

High-Throughput Analysis

[Analysis of Protein Interactions with Immobilized Peptide Arrays Synthesized on Membrane Supports]

[Assays with Protein Arrays]

[Copy Number Variation Detection via High-Density SNP Genotyping]

[Gateway-Compatible Yeast One-Hybrid Screens]

[In Vitro Screening for Regulated Transcription Factors with Differential Display of DNA-Binding Proteins (DDDP)]

[Laboratory Methods for High-Throughput Genotyping]

[Methylated CpG Island Amplification and Microarray (MCAM) for High-Throughput Analysis of DNA Methylation]

[Mouse Mutagenesis Using N-Ethyl-N-Nitrosourea (ENU)]

[Native Chromatin Preparation and Illumina/Solexa Library Construction]

[Production of Endoribonuclease-Prepared Short Interfering RNAs (esiRNAs) for Specific and Effective Gene Silencing in Mammalian Cells]

Imaging / Microscopy

[A Sealed Preparation for Long-Term Observations of Cultured Cells]

[Computational Image Analysis of Cellular Dynamics: A Case Study Based on Particle Tracking]

[Development of Mammalian Cell Lines with lac Operator-Tagged Chromosomes]

[Dye Loading with Patch Pipettes]

[Ex Ovo Electroporation of DNA Vectors into Pre-gastrulation Avian Embryos]

[Fate-Mapping Technique: Using Carbocyanine Dyes for Vital Labeling of Cells in Gastrula-Stage Mouse Embryos Cultured in Vitro]

[Fluorescent Protein Tracking and Detection: Fluorescent Protein Structure and Color Variants]

[Live-Cell Imaging of GFP in Plants]

[Live Imaging of Caenorhabditis elegans: Examples]

[Microinjection of Protein Samples]

[Photoactivation-Based Labeling and In Vivo Tracking of RNA Molecules in the Nucleus]

[Preparation of Complex DNA Probe Sets for 3D FISH with up to Six Different Fluorochromes]

[Preparation of Rodent Hippocampal Slice Cultures]

[Selection of Appropriate Imaging Equipment and Methodology for Live Cell Imaging in Drosophila]

[Studying Mitosis in Cultured Mammalian Cells]

[Use of Fluorescence In Situ Hybridization and the daime Image Analysis Program for the Cultivation-Independent Quantification of Microorganisms in Environmental and Medical Samples]

Immunology

[Bone Marrow-Derived Macrophages (BMM): Isolation and Applications]

[Cutaneous Two-Stage Chemical Carcinogenesis]

[Dual-Color ELISPOT Assay for the Simultaneous Detection of IL-2 and IFN-γ Secreting T Cells]

[Fetal Thymus Organ Culture]

[The OP9-DL1 System: Generation of T-Lymphocytes from Embryonic or Hematopoietic Stem Cells In Vitro]

Laboratory Organisms

[Ex Ovo Electroporation of DNA Vectors into Pre-gastrulation Avian Embryos]

[Fate-Mapping Technique: Using Carbocyanine Dyes for Vital Labeling of Cells in Gastrula-Stage Mouse Embryos Cultured in Vitro]

[Immunohistochemistry of Whole-Mount Mouse Embryos]

[Injection of dsRNA into Drosophila Embryos for RNA Interference (RNAi)]

[In Planta Transformation of Arabidopsis]

[Isolation and Whole-Cell Patch Clamping of Arabidopsis Guard Cell Protoplasts]

[Karyotyping Mouse Cells]

[Live-Cell Imaging of GFP in Plants]

[Live Imaging of Caenorhabditis elegans: Examples]

[Maintenance of a Drosophila Laboratory: General Procedures]

[Mapping Protein Distributions on Polytene Chromosomes by Immunostaining]

[Measurement of Courtship Behavior in Drosophila melanogaster]

[Mouse Mutagenesis Using N-Ethyl-N-Nitrosourea (ENU)]

[Planarians: A Versatile and Powerful Model System for Molecular Studies of Regeneration, Adult Stem Cell Regulation, Aging, and Behavior]

[Preparation of Rodent Hippocampal Slice Cultures]

[Selection of Appropriate Imaging Equipment and Methodology for Live Cell Imaging in Drosophila]

[SIRT Combines Homologous Recombination, Site-Specific Integration, and Bacterial Recombineering for Targeted Mutagenesis in Drosophila]

[Staining Whole Mouse Embryos for β-Galactosidase (lacZ) Activity]

[The Genus Antirrhinum (Snapdragon): A Flowering Plant Model for Evolution and Development]

[Transcript In Situ Hybridization of Whole-Mount Embryos for Phenotype Analysis of RNAi-Treated Drosophila]

[Whole-Mount In Situ Hybridization of RNA Probes to Plant Tissues]

[Xenopus laevis Keller Explants]

Molecular Biology

[Analysis of Protein Interactions with Immobilized Peptide Arrays Synthesized on Membrane Supports]

[Analysis of RNA-Protein Complexes by RNA Coimmunoprecipitation and RT-PCR Analysis from Caenorhabditis elegans]

[Assay for Human Rad51-Mediated DNA Displacement Loop Formation]

[Chromatin Immunoprecipitation (ChIP)]

[Chromatin Immunoprecipitation (ChIP) of Protein Complexes: Mapping of Genomic Targets of Nuclear Proteins in Cultured Cells]

[Chromatin Immunopreciptation (ChIP) on Unfixed Chromatin from Cells and Tissues to Analyze Histone Modifications]

[Combined 3C-ChIP-Cloning (6C) Assay: A Tool to Unravel Protein-Mediated Genome Architecture]

[Combined Flow Cytometric Measurement of Two Cell-Surface Antigens and DNA-RNA Content]

[Construction of Gene-Targeting Vectors by Recombineering]

[DNA Immunoprecipitation (DIP) for the Determination of DNA-Binding Specificity]

[Cutaneous Two-Stage Chemical Carcinogenesis]

[Design and Cloning of an shRNA into a Lentiviral Silencing Vector: Version A]

[Development of Mammalian Cell Lines with lac Operator-Tagged Chromosomes]

[Ex Ovo Electroporation of DNA Vectors into Pre-gastrulation Avian Embryos]

[Fluorescence In Situ Hybridization for the Identification of Environmental Microbes]

[Gateway-Compatible Yeast One-Hybrid Screens]

[Genotyping by Oligonucleotide Ligation Assay (OLA)]

[Immunohistochemistry of Whole-Mount Mouse Embryos]

[In Vitro Screening for Regulated Transcription Factors with Differential Display of DNA-Binding Proteins (DDDP)]

[Injection of dsRNA into Drosophila Embryos for RNA Interference (RNAi)]

[Mapping Protein Distributions on Polytene Chromosomes by Immunostaining]

[Methylated CpG Island Amplification and Microarray (MCAM) for High-Throughput Analysis of DNA Methylation]

[Microinjection of dsRNA into Mouse Oocytes and Early Embryos]

[Mouse Mutagenesis Using N-Ethyl-N-Nitrosourea (ENU)]

[Native Chromatin Preparation and Illumina/Solexa Library Construction]

[Optimization and Troubleshooting in PCR]

[Photoactivation-Based Labeling and In Vivo Tracking of RNA Molecules in the Nucleus]

[Preparation of Complex DNA Probe Sets for 3D FISH with up to Six Different Fluorochromes]

[Production of Endoribonuclease-Prepared Short Interfering RNAs (esiRNAs) for Specific and Effective Gene Silencing in Mammalian Cells]

[Preparation of GST Fusion Proteins]

[Quantitation of DNA and RNA]

[Quantitative Real-Time RT-PCR (qRT-PCR) of Zebrafish Transcripts: Optimization of RNA Extraction, Quality Control Considerations, and Data Analysis]

[Regulating Protein Stability in Mammalian Cells Using Small Molecules]

[SIRT Combines Homologous Recombination, Site-Specific Integration, and Bacterial Recombineering for Targeted Mutagenesis in Drosophila]

[SNP Mining from Maize 454 EST Sequences]

[Staining Whole Mouse Embryos for β-Galactosidase (lacZ) Activity]

[Transcript In Situ Hybridization of Whole-Mount Embryos for Phenotype Analysis of RNAi-Treated Drosophila]

[Virus-Induced Gene Silencing as a Tool for Delivery of dsRNA into Plants]

[Whole-Mount In Situ Hybridization of RNA Probes to Plant Tissues]

Neuroscience

[Cultures of Cerebellar Granule Neurons]

[Dye Loading with Patch Pipettes]

[Isolation, Culture, and Differentiaton of Progenitor Cells from the Central Nervous System]

[Measurement of Courtship Behavior in Drosophila melanogaster]

[Preparation of Rodent Hippocampal Slice Cultures]

Plant Biology

[In Planta Transformation of Arabidopsis]

[Isolation and Whole-Cell Patch Clamping of Arabidopsis Guard Cell Protoplasts]

[Live-Cell Imaging of GFP in Plants]

[Whole-Mount In Situ Hybridization of RNA Probes to Plant Tissues]

[SNP Mining from Maize 454 EST Sequences]

[The Genus Antirrhinum (Snapdragon): A Flowering Plant Model for Evolution and Development]

[Virus-Induced Gene Silencing as a Tool for Delivery of dsRNA into Plants]

Polymerase Chain Reaction (PCR)

[Analysis of RNA-Protein Complexes by RNA Coimmunoprecipitation and RT-PCR Analysis from Caenorhabditis elegans]

[Genotyping by Oligonucleotide Ligation Assay (OLA)]

[Methylated CpG Island Amplification and Microarray (MCAM) for High-Throughput Analysis of DNA Methylation]

[Optimization and Troubleshooting in PCR]

[Preparation of Complex DNA Probe Sets for 3D FISH with up to Six Different Fluorochromes]

[Quantitative Real-Time RT-PCR (qRT-PCR) of Zebrafish Transcripts: Optimization of RNA Extraction, Quality Control Considerations, and Data Analysis]

Proteins and Proteomics

[Analysis of Complex Protein Mixtures Using Multidimensional Protein Identification Technology (MuDPIT)]

[Analysis of Protein Interactions with Immobilized Peptide Arrays Synthesized on Membrane Supports]

[Analysis of RNA-Protein Complexes by RNA Coimmunoprecipitation and RT-PCR Analysis from Caenorhabditis elegans]

[Assays with Protein Arrays]

[Bimolecular Affinity Purification (BAP): Tandem Affinity Purification Using Two Protein Baits]

[Chromatin Immunoprecipitation (ChIP)]

[Chromatin Immunoprecipitation (ChIP) of Protein Complexes: Mapping of Genomic Targets of Nuclear Proteins in Cultured Cells]

[Chromatin Immunopreciptation (ChIP) on Unfixed Chromatin from Cells and Tissues to Analyze Histone Modifications]

[Combined 3C-ChIP-Cloning (6C) Assay: A Tool to Unravel Protein-Mediated Genome Architecture]

[Development of Mammalian Cell Lines with lac Operator-Tagged Chromosomes]

[Fluorescent Protein Tracking and Detection: Fluorescent Protein Structure and Color Variants]

[Gateway-Compatible Yeast One-Hybrid Screens]

[HPLC Separation of Digested Proteins and Preparation for Matrix-Assisted Laser Desorption/Ionization Analysis]

[In Vitro Assays for the Extracellular Matrix Protein-Regulated Extravasation Process]

[In Vitro Screening for Regulated Transcription Factors with Differential Display of DNA-Binding Proteins (DDDP)]

[In Vitro Sumoylation of Recombinant Proteins and Subsequent Purification for Use in Enzymatic Assays]

[In Vivo Isotopic Labeling of Proteins for Quantitative Proteomics]

[Injection of dsRNA into Drosophila Embryos for RNA Interference (RNAi)]

[Mapping Protein Distributions on Polytene Chromosomes by Immunostaining]

[Microinjection of Protein Samples]

[Preparation of GST Fusion Proteins]

[Regulating Protein Stability in Mammalian Cells Using Small Molecules]

[Systematic Monitoring of Protein Complex Composition and Abundance by Blue-Native PAGE]

RNA Interference (RNAi)/siRNA

[Design and Cloning of an shRNA into a Lentiviral Silencing Vector: Version A]

[Injection of dsRNA into Drosophila Embryos for RNA Interference (RNAi)]

[Microinjection of dsRNA into Mouse Oocytes and Early Embryos]

[Production of Endoribonuclease-Prepared Short Interfering RNAs (esiRNAs) for Specific and Effective Gene Silencing in Mammalian Cells]

[Transcript In Situ Hybridization of Whole-Mount Embryos for Phenotype Analysis of RNAi-Treated Drosophila]

[Virus-Induced Gene Silencing as a Tool for Delivery of dsRNA into Plants]

Stem Cells

[Culturing Human Embryonic Stem Cells in Feeder-Free Conditions]

[Hematopoietic Stem Cell Targeting with Surface-Engineered Lentiviral Vectors]

[Isolation, Culture, and Differentiaton of Progenitor Cells from the Central Nervous System]

[Noninvasive Human Nuclear Transfer with Embryonic Stem Cells]

[The OP9-DL1 System: Generation of T-Lymphocytes from Embryonic or Hematopoietic Stem Cells In Vitro]

[Use of the Sleeping Beauty Transposon System for Stable Gene Expression in Mouse Embryonic Stem Cells]

Transgenic Technology

[Construction and Characterization of Adenovirus Vectors]

[Construction of Gene-Targeting Vectors by Recombineering]

[Ex Ovo Electroporation of DNA Vectors into Pre-gastrulation Avian Embryos]

[Injection of dsRNA into Drosophila Embryos for RNA Interference (RNAi)]

[In Planta Transformation of Arabidopsis]

[Microinjection of dsRNA into Mouse Oocytes and Early Embryos]

[SIRT Combines Homologous Recombination, Site-Specific Integration, and Bacterial Recombineering for Targeted Mutagenesis in Drosophila]

[Staining Whole Mouse Embryos for β-Galactosidase (lacZ) Activity]

[Use of the Sleeping Beauty Transposon System for Stable Gene Expression in Mouse Embryonic Stem Cells]

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