CSH Protocols, Table of Contents
Primary Archive, Section 3

May 2006

Protocols

Preparation of DNA for Pulsed-field Gel Electrophoresis: Isolation of DNA from Mammalian Cells and Tissues
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4030
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Restriction Endonuclease Digestion of DNA in Agarose Plugs
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4031
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Pulsed-field Gel Electrophoresis via Transverse Alternating Field Electrophoresis Gels
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4032
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Pulsed-field Gel Electrophoresis via Contour-clamped Homogeneous Electric Field Gels
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4033
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Retrieval of DNA Fragments from Pulsed-field Gels following DNA Concentration
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4035
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Isolation of High-molecular-weight DNA from Mammalian Cells Using Proteinase K and Phenol
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4036
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Isolation of DNA from Mammalian Cells by Spooling
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4037
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Preparation of Genomic DNA from Mouse Tails and Other Small Samples
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4038
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Rapid Isolation of Yeast DNA
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4039
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Southern Blotting: Capillary Transfer of DNA to Membranes
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4040
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Southern Blotting: Simultaneous Transfer of DNA from a Single Agarose Gel to Two Membranes
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4043
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Southern Hybridization of Radiolabeled Probes to Nucleic Acids Immobilized on Membranes
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4044
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Purification of RNA from Cells and Tissues by Acid Phenol-Guanidinium Thiocyanate-Chloroform Extraction
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4045
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Selection of Poly(A)+ RNA by Oligo(dT)-Cellulose Chromatography
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4047
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Selection of Poly(A)+ RNA by Batch Chromatography
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4048
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Separation of RNA According to Size: Electrophoresis of RNA through Agarose Gels Containing Formaldehyde
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4050
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Dot and Slot Hybridization of Purified RNA
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4052
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Mapping RNA with Nuclease S1
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4053
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Ribonuclease Protection: Mapping RNA with Ribonuclease and Radiolabeled RNA Probes
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4054
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Analysis of RNA by Primer Extension
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4055
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A Single-step Method for the Simultaneous Preparation of DNA, RNA, and Protein from Cells and Tissues
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4056
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Separation of RNA According to Size: Electrophoresis of Glyoxylated RNA through Agarose Gels
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4057
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Transfer and Fixation of Denatured RNA to Membranes
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4060
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Synthesis of Single-stranded DNA Probes of Defined Length from Bacteriophage M13 Templates
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4061
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Purification of Synthetic Oligonucleotides by Polyacrylamide Gel Electrophoresis
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4063
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Purification of Radiolabeled Oligonucleotides by Chromatography on a Sep-Pak C18 Column
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4064
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Construction of cDNA Libraries Stage 1: Synthesis of First-strand cDNA Catalyzed by Reverse Transcriptase
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4065
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Construction and Screening of Eukaryotic Expression Libraries • Stage 1: Construction of cDNA Libraries in Eukaryotic Expression Vectors
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4068
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Construction and Screening of Eukaryotic Expression Libraries • Stage 2: Screening cDNA Libraries Constructed in Eukaryotic Expression Vectors
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4069
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Construction of cDNA Libraries • Stage 3: Methylation of cDNA
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4073
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Construction of cDNA Libraries Stage 6: Ligation of cDNA to Bacteriophage {lambda} Arms
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4074
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Exon Trapping and Amplification • Stage 1: Construction of the Library
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4075
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Exon Trapping and Amplification • Stage 4: Reverse Transcriptase-PCR
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4076
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Direct Selection of cDNAs with Large Genomic DNA Clones
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4077
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Generation of Sets of Nested Deletion Mutants with Exonuclease III
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4078
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Screening Expression Libraries Constructed in Plasmid Vectors
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4079
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Generation of a Library of Randomly Overlapping DNA Inserts
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4081
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Direct Retrieval of DNA Fragments from Pulsed-field Gels
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4083
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Preparation of Plasmid DNA by Alkaline Lysis with SDS: Minipreparation
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4084
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Expression of Cloned Genes in E. coli Using IPTG-inducible Promoters
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4085
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Expression of Cloned Genes in E. coli Using the Bacteriophage {lambda} pL Promoter
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4086
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Purification of Maltose-binding Fusion Proteins by Affinity Chromatography on Amylose Resin
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4087
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Purification of Histidine-tagged Proteins by Immobilized Ni2+ Absorption Chromatography
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4088
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Purification of Expressed Proteins from Inclusion Bodies
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4089
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Preparation of Plasmid DNA by Alkaline Lysis with SDS: Maxipreparation
Joseph Sambrook and David W. Russell
CSH Protocols; 2006; doi:10.1101/pdb.prot4090
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Dealing with Carryover Contamination in PCR: An Enzymatic Strategy
Kyusung Park and Jun Lee
CSH Protocols; 2006; doi:10.1101/pdb.prot4092
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PCR Amplification of Highly GC-Rich Regions
Lise Lotte Hansen and Just Justesen
CSH Protocols; 2006; doi:10.1101/pdb.prot4093
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Long and Accurate PCR
Wayne M. Barnes
CSH Protocols; 2006; doi:10.1101/pdb.prot4094
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Nonradioactive Cycle Sequencing of PCR-Amplified DNA
Susan R. Haynes
CSH Protocols; 2006; doi:10.1101/pdb.prot4095
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Purification of Genomic DNA from Whole Blood: A Solution-Based Method
Craig Smith, Paul Otto, Rex Bitner, and Gary Shiels
CSH Protocols; 2006; doi:10.1101/pdb.prot4096
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A Silica Membrane-Based Method for the Isolation of Genomic DNA from Tissues and Cultured Cells
Craig Smith, Paul Otto, Rex Bitner, and Gary Shiels
CSH Protocols; 2006; doi:10.1101/pdb.prot4097
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DNA IQ Isolation of Genomic DNA from Stains and Buccal Swabs
Craig Smith, Paul Otto, Rex Bitner, and Gary Shiels
CSH Protocols; 2006; doi:10.1101/pdb.prot4098
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A Silica-Based Method for Purifying PCR Fragments from Agarose Gels
Craig Smith, Paul Otto, Rex Bitner, and Gary Shiels
CSH Protocols; 2006; doi:10.1101/pdb.prot4099
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A Magnetic Particle-Based Method for Purifying PCR Products from Solution
Craig Smith, Paul Otto, Rex Bitner, and Gary Shiels
CSH Protocols; 2006; doi:10.1101/pdb.prot4100
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Dye Terminator Cleanup for Automated DNA Sequencing Reactions
Craig Smith, Paul Otto, Rex Bitner, and Gary Shiels
CSH Protocols; 2006; doi:10.1101/pdb.prot4101
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Preparation of RNA from Plant Tissue Using Guanidinium Isothiocyanate/Cesium Chloride Ultracentrifugation
Michael A. Connolly, Peter A. Clausen, and James G. Lazar
CSH Protocols; 2006; doi:10.1101/pdb.prot4102
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Preparation of RNA from Paraffin-Embedded Fixed Tissue Using Trizol
Michael A. Connolly, Peter A. Clausen, and James G. Lazar
CSH Protocols; 2006; doi:10.1101/pdb.prot4103
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Purification of RNA from Animal Cells Using Trizol
Michael A. Connolly, Peter A. Clausen, and James G. Lazar
CSH Protocols; 2006; doi:10.1101/pdb.prot4104
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Preparation of RNA from Plant Tissue Using Trizol
Michael A. Connolly, Peter A. Clausen, and James G. Lazar
CSH Protocols; 2006; doi:10.1101/pdb.prot4105
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Purification of RNA from Plant Tissue Using the Concert Plant Reagent
Michael A. Connolly, Peter A. Clausen, and James G. Lazar
CSH Protocols; 2006; doi:10.1101/pdb.prot4106
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Laser Capture Microdissection (LCM): Preparation and Sectioning of Frozen Tissue Blocks and Purification of RNA from Isolated Cells
Motoko Morimoto, Masahiro Morimoto, Jeanette Whitmire, Robert A. Star, Joseph F. Urban, Jr., and William C. Gause
CSH Protocols; 2006; doi:10.1101/pdb.prot4107
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cDNA Synthesis and Real-Time PCR Using RNA from Laser-Captured Cells
Motoko Morimoto, Masahiro Morimoto, Jeanette Whitmire, Robert A. Star, Joseph F. Urban, Jr., and William C. Gause
CSH Protocols; 2006; doi:10.1101/pdb.prot4108
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Relative RT-PCR: Determining the Linear Range of Amplification and Optimizing the Primers:Competimers Ratio
Renée M. Horner
CSH Protocols; 2006; doi:10.1101/pdb.prot4109
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Competitive RT-PCR: Preparation of Competitor RNA
Renée M. Horner
CSH Protocols; 2006; doi:10.1101/pdb.prot4110
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Competitive RT-PCR: Estimation of Copy Number
Renée M. Horner
CSH Protocols; 2006; doi:10.1101/pdb.prot4111
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Real-Time PCR
Wolfgang Kusser, Sandrine Javorschi, and Martin A. Gleeson
CSH Protocols; 2006; doi:10.1101/pdb.prot4112
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Multiplex Real-Time PCR
 Wolfgang Kusser, Sandrine Javorschi, and Martin A. Gleeson
CSH Protocols; 2006; doi:10.1101/pdb.prot4113
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Real-Time RT-PCR: cDNA Synthesis
Wolfgang Kusser, Sandrine Javorschi, and Martin A. Gleeson
CSH Protocols; 2006; doi:10.1101/pdb.prot4114
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Amplification of RNA: High-Temperature Reverse Transcription and DNA Amplification with a Magnesium-Activated Thermostable DNA Polymerase
Edward S. Smith, Alvin K. Li, Alice M. Wang, David H. Gelfand, and Thomas W. Myers
CSH Protocols; 2006; doi:10.1101/pdb.prot4115
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Loss of Heterozygosity: A Multiplex PCR Method to Define a Narrow Deleted Chromosomal Region of a Tumor Genome
Lise Hansen and Just Justesen
CSH Protocols; 2006; doi:10.1101/pdb.prot4117
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Single-Strand Conformation Polymorphism Analysis
Anne E. Jedlicka and Steven R. Kleeberger
CSH Protocols; 2006; doi:10.1101/pdb.prot4118
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Reverse Transcriptase In Situ PCR
Gerard J. Nuovo
CSH Protocols; 2006; doi:10.1101/pdb.prot4119
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Mutation Detection by Solid-Phase Chemical Cleavage of Mismatches Using Radioactive Probes
Lisa Lotte Hansen, Justesen Just, Andreana Lambrinakos, and Richard G.H. Cotton
CSH Protocols; 2006; doi:10.1101/pdb.prot4120
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Hybridization and Detection Using the HC ExpressArray Kit
Joan M. Zakel
CSH Protocols; 2006; doi:10.1101/pdb.prot4122
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Extraction and Purification of RNA from Tissue-Cultured Cells for Fluorescent mRNA Differential Display
Jeffrey S. Fisher, Jonathan Meade, Jamie Walden, Zhen Guo, and Peng Liang
CSH Protocols; 2006; doi:10.1101/pdb.prot4123
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Extraction and Purification of RNA from Tissue Samples for Fluorescent mRNA Differential Display
Jeffrey S. Fisher, Jonathan Meade, Jamie Walden, Zhen Guo, and Peng Liang
CSH Protocols; 2006; doi:10.1101/pdb.prot4124
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Extraction and Purification of RNA from Blood Samples for Fluorescent mRNA Differential Display
Jeffrey S. Fisher, Jonathan Meade, Jamie Walden, Zhen Guo, and Peng Liang
CSH Protocols; 2006; doi:10.1101/pdb.prot4125
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Removal of Genomic DNA from Total RNA for Use in Fluorescent mRNA Differential Display
Jeffrey S. Fisher, Jonathan Meade, Jamie Walden, Zhen Guo, and Peng Liang
CSH Protocols; 2006; doi:10.1101/pdb.prot4126
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Preparation of a Denaturing Agarose Gel for the Analysis of RNA Samples
Jeffrey S. Fisher, Jonathan Meade, Jamie Walden, Zhen Guo, and Peng Liang
CSH Protocols; 2006; doi:10.1101/pdb.prot4127
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FDD PCR, Identification and Analysis of Differentially Expressed cDNAs
Jeffrey S. Fisher, Jonathan Meade, Jamie Walden, Zhen Guo, and Peng Liang
CSH Protocols; 2006; doi:10.1101/pdb.prot4128
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PCR-Based Screening of DNA Libraries
David I. Israel
CSH Protocols; 2006; doi:10.1101/pdb.prot4129
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3'-End cDNA Amplification Using Classic RACE
Michael A. Frohman
CSH Protocols; 2006; doi:10.1101/pdb.prot4130
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5'-End cDNA Amplification Using Classic RACE
Michael A. Frohman
CSH Protocols; 2006; doi:10.1101/pdb.prot4131
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5'-End cDNA Amplification Using New RACE
Michael A. Frohman
CSH Protocols; 2006; doi:10.1101/pdb.prot4132
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Cap-Switching RACE
Michael A. Frohman
CSH Protocols; 2006; doi:10.1101/pdb.prot4133
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Use of PCR to Prepare a Double-Stranded DNA Library Encoding Random Peptides
John L. Joyal, Jinwei Jiang, and David I. Israel
CSH Protocols; 2006; doi:10.1101/pdb.prot4135
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Synthesis of DNA Libraries: Use of PCR to Analyze Ligation Substrates and Products
John L. Joyal, Jinwei Jiang, and David I. Israel
CSH Protocols; 2006; doi:10.1101/pdb.prot4136
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Use of PCR for Quality Control of a Peptide DNA Library
John L. Joyal, Jinwei Jiang, and David I. Israel
CSH Protocols; 2006; doi:10.1101/pdb.prot4137
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Use of PCR for Quality Control of a Genomic DNA Library
John L. Joyal, Jinwei Jiang, and David I. Israel
CSH Protocols; 2006; doi:10.1101/pdb.prot4138
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Bidirectional Cloning of PCR Products
Gina L. Costa and Michael P. Weiner
CSH Protocols; 2006; doi:10.1101/pdb.prot4139
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Directional Cloning of PCR Products
Gina L. Costa and Michael P. Weiner
CSH Protocols; 2006; doi:10.1101/pdb.prot4140
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Colony PCR
Gina L. Costa and Michael P. Weiner
CSH Protocols; 2006; doi:10.1101/pdb.prot4141
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Ribocloning: DNA Cloning and Gene Construction Using PCR Primers Terminated with a Ribonucleotide
Wayne M. Barnes
CSH Protocols; 2006; doi:10.1101/pdb.prot4142
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Mutagenic PCR
R. Craig Cadwell and Gerald F. Joyce
CSH Protocols; 2006; doi:10.1101/pdb.prot4143
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Rapid PCR Site-Directed Mutagenesis
Gina L. Costa and Michael P. Weiner
CSH Protocols; 2006; doi:10.1101/pdb.prot4144
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High-Efficiency Transformation of Yeast
David C. Amberg, Daniel J. Burke, and Jeffrey N. Strathern
CSH Protocols; 2006; doi:10.1101/pdb.prot4145
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"Quick and Dirty" Plasmid Transformation of Yeast Colonies
David C. Amberg, Daniel J. Burke, and Jeffrey N. Strathern
CSH Protocols; 2006; doi:10.1101/pdb.prot4146
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Yeast DNA Isolation: Midiprep
David C. Amberg, Daniel J. Burke, and Jeffrey N. Strathern
CSH Protocols; 2006; doi:10.1101/pdb.prot4147
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Yeast DNA Isolation: Miniprep
David C. Amberg, Daniel J. Burke, and Jeffrey N. Strathern
CSH Protocols; 2006; doi:10.1101/pdb.prot4148
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Isolation of Yeast Genomic DNA for Southern Blot Analysis
David C. Amberg, Daniel J. Burke, and Jeffrey N. Strathern
CSH Protocols; 2006; doi:10.1101/pdb.prot4149
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