CSH Protocols, Table of Contents
Primary Archive, Section 4

May 2006

Protocols

Isolation of Plasmid DNA from Yeast Cells: A Ten-Minute Preparation
David C. Amberg, Daniel J. Burke, and Jeffrey N. Strathern
CSH Protocols; 2006; doi:10.1101/pdb.prot4150
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Preparation of Genomic DNA from Yeast Using Glass Beads
David C. Amberg, Daniel J. Burke, and Jeffrey N. Strathern
CSH Protocols; 2006; doi:10.1101/pdb.prot4151
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Yeast Protein Extracts
David C. Amberg, Daniel J. Burke, and Jeffrey N. Strathern
CSH Protocols; 2006; doi:10.1101/pdb.prot4152
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Tandem Affinity Protein (TAP) Purification from Yeast
David C. Amberg, Daniel J. Burke, and Jeffrey N. Strathern
CSH Protocols; 2006; doi:10.1101/pdb.prot4153
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Yeast RNA Isolation: Large-Scale
David C. Amberg, Daniel J. Burke, and Jeffrey N. Strathern
CSH Protocols; 2006; doi:10.1101/pdb.prot4154
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Yeast RNA Isolation: Small-Scale
David C. Amberg, Daniel J. Burke, and Jeffrey N. Strathern
CSH Protocols; 2006; doi:10.1101/pdb.prot4155
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Hydroxylamine Mutagenesis of Plasmid DNA
David C. Amberg, Daniel J. Burke, and Jeffrey N. Strathern
CSH Protocols; 2006; doi:10.1101/pdb.prot4156
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Assay of ß-Galactosidase in Yeast: Assay of Crude Extracts
David C. Amberg, Daniel J. Burke, and Jeffrey N. Strathern
CSH Protocols; 2006; doi:10.1101/pdb.prot4157
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Assay of ß-Galactosidase in Yeast: Permeabilized Cell Assay
David C. Amberg, Daniel J. Burke, and Jeffrey N. Strathern
CSH Protocols; 2006; doi:10.1101/pdb.prot4158
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Assay of ß-Galactosidase in Yeast: Freeze/Thaw Assay by Chemiluminescence in Microcentrifuge Tubes
David C. Amberg, Daniel J. Burke, and Jeffrey N. Strathern
CSH Protocols; 2006; doi:10.1101/pdb.prot4159
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Assay of ß-Galactosidase in Yeast: Freeze/Thaw Assay by Chemiluminescence in 96-Well Plates
David C. Amberg, Daniel J. Burke, and Jeffrey N. Strathern
CSH Protocols; 2006; doi:10.1101/pdb.prot4160
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Plate Assay for Carboxypeptidase Y in Yeast Cells
David C. Amberg, Daniel J. Burke, and Jeffrey N. Strathern
CSH Protocols; 2006; doi:10.1101/pdb.prot4161
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Random Spore Analysis in Yeast
David C. Amberg, Daniel J. Burke, and Jeffrey N. Strathern
CSH Protocols; 2006; doi:10.1101/pdb.prot4162
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Yeast Vital Stains: DAPI Stain of Nuclear and Mitochondrial DNA
David C. Amberg, Daniel J. Burke, and Jeffrey N. Strathern
CSH Protocols; 2006; doi:10.1101/pdb.prot4163
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Yeast Vital Stains: Visualizing Mitochondria with DiOC6 or DiIC5(3)
David C. Amberg, Daniel J. Burke, and Jeffrey N. Strathern
CSH Protocols; 2006; doi:10.1101/pdb.prot4164
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Yeast Vital Stains: Visualizing Vacuoles and Endocytic Compartments with FM4-64
David C. Amberg, Daniel J. Burke, and Jeffrey N. Strathern
CSH Protocols; 2006; doi:10.1101/pdb.prot4165
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Yeast Vital Stains: Calcofluor Staining of Chitin and Bud Scars
David C. Amberg, Daniel J. Burke, and Jeffrey N. Strathern
CSH Protocols; 2006; doi:10.1101/pdb.prot4166
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Yeast Immunofluorescence
David C. Amberg, Daniel J. Burke, and Jeffrey N. Strathern
CSH Protocols; 2006; doi:10.1101/pdb.prot4167
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Actin Staining in Fixed Yeast Cells
David C. Amberg, Daniel J. Burke, and Jeffrey N. Strathern
CSH Protocols; 2006; doi:10.1101/pdb.prot4168
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PCR-Mediated Gene Disruption: One-Step Method
David C. Amberg, Daniel J. Burke, and Jeffrey N. Strathern
CSH Protocols; 2006; doi:10.1101/pdb.prot4169
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Yeast Colony PCR
David C. Amberg, Daniel J. Burke, and Jeffrey N. Strathern
CSH Protocols; 2006; doi:10.1101/pdb.prot4170
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Inducing Yeast Cell Synchrony: {alpha}-Factor Arrest Using Low Cell Concentration
David C. Amberg, Daniel J. Burke, and Jeffrey N. Strathern
CSH Protocols; 2006; doi:10.1101/pdb.prot4171
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Inducing Yeast Cell Synchrony: {alpha}-Factor Arrest Using Low pH
David C. Amberg, Daniel J. Burke, and Jeffrey N. Strathern
CSH Protocols; 2006; doi:10.1101/pdb.prot4172
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Inducing Yeast Cell Synchrony: {alpha}-Factor Arrest Using bar1 Mutants
David C. Amberg, Daniel J. Burke, and Jeffrey N. Strathern
CSH Protocols; 2006; doi:10.1101/pdb.prot4173
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Inducing Yeast Cell Synchrony: Hydroxyurea Arrest
David C. Amberg, Daniel J. Burke, and Jeffrey N. Strathern
CSH Protocols; 2006; doi:10.1101/pdb.prot4174
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Inducing Yeast Cell Synchrony: Nocodazole Arrest
David C. Amberg, Daniel J. Burke, and Jeffrey N. Strathern
CSH Protocols; 2006; doi:10.1101/pdb.prot4175
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Inducing Yeast Cell Synchrony: Dilution of Stationary-Phase Cultures
David C. Amberg, Daniel J. Burke, and Jeffrey N. Strathern
CSH Protocols; 2006; doi:10.1101/pdb.prot4176
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Chromatin Immunoprecipitation in Yeast
David C. Amberg, Daniel J. Burke, and Jeffrey N. Strathern
CSH Protocols; 2006; doi:10.1101/pdb.prot4177
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Preparation of Yeast Cells for Flow Cytometry
David C. Amberg, Daniel J. Burke, and Jeffrey N. Strathern
CSH Protocols; 2006; doi:10.1101/pdb.prot4178
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Logarithmic Growth
David C. Amberg, Daniel J. Burke, and Jeffrey N. Strathern
CSH Protocols; 2006; doi:10.1101/pdb.prot4179
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Ethyl Methane Sulfonate (EMS) Mutagenesis
David C. Amberg, Daniel J. Burke, and Jeffrey N. Strathern
CSH Protocols; 2006; doi:10.1101/pdb.prot4180
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Tetrad Dissection
David C. Amberg, Daniel J. Burke, and Jeffrey N. Strathern
CSH Protocols; 2006; doi:10.1101/pdb.prot4181
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Making a Tetrad Dissection Needle
David C. Amberg, Daniel J. Burke, and Jeffrey N. Strathern
CSH Protocols; 2006; doi:10.1101/pdb.prot4182
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Picking Zygotes
David C. Amberg, Daniel J. Burke, and Jeffrey N. Strathern
CSH Protocols; 2006; doi:10.1101/pdb.prot4183
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Determining Plating Efficiency in Yeast: Indirect Method
David C. Amberg, Daniel J. Burke, and Jeffrey N. Strathern
CSH Protocols; 2006; doi:10.1101/pdb.prot4184
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Determining Plating Efficiency in Yeast: Direct Method
David C. Amberg, Daniel J. Burke, and Jeffrey N. Strathern
CSH Protocols; 2006; doi:10.1101/pdb.prot4185
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Measuring Yeast Cell Density by Spectrophotometry
David C. Amberg, Daniel J. Burke, and Jeffrey N. Strathern
CSH Protocols; 2006; doi:10.1101/pdb.prot4186
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The Tap-Fill Method for Dry Packing Columns of Rigid Solids
Richard J. Simpson
CSH Protocols; 2006; doi:10.1101/pdb.prot4187
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Preparation of Vectors for High-Throughput Screening of Soluble Recombinant Proteins
Ting-Fang Wang and Andrew H.-J. Wang
CSH Protocols; 2006; doi:10.1101/pdb.prot4188
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Preparation of Sticky-End PCR Products and Ligation into Expression Vectors for High-Throughput Screening of Soluble Recombinant Proteins
Ting-Fang Wang and Andrew H.-J. Wang
CSH Protocols; 2006; doi:10.1101/pdb.prot4189
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Induction and Screening of Soluble Fusion Proteins in Bacterial Cells
Ting-Fang Wang and Andrew H.-J. Wang
CSH Protocols; 2006; doi:10.1101/pdb.prot4190
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Selection of an Ion Exchanger: Determining the pI of a Protein Using the Titration Curve Method
Bengt Westerlund
CSH Protocols; 2006; doi:10.1101/pdb.prot4191
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Selection of an Ion Exchanger: Determining the pI of a Protein Using Isoelectric Focusing
Bengt Westerlund
CSH Protocols; 2006; doi:10.1101/pdb.prot4192
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Selection of an Ion Exchanger: Determining the pI of a Protein Using the Test Tube Method
Bengt Westerlund
CSH Protocols; 2006; doi:10.1101/pdb.prot4193
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Selection of an Ion Exchanger: Determining the pI of a Protein Using the Trial-and-Error Method
Bengt Westerlund
CSH Protocols; 2006; doi:10.1101/pdb.prot4194
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Preparation of an Ion-Exchange Column
Bengt Westerlund
CSH Protocols; 2006; doi:10.1101/pdb.prot4195
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Separating Proteins Using Ion-Exchange Chromatography
Bengt Westerlund
CSH Protocols; 2006; doi:10.1101/pdb.prot4196
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Packing a Size-Exclusion Column
Helena Hedlund
CSH Protocols; 2006; doi:10.1101/pdb.prot4197
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Preparative Size-Exclusion Chromatography
Helena Hedlund
CSH Protocols; 2006; doi:10.1101/pdb.prot4198
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Desalting and Buffer Exchange of Proteins Using Size-Exclusion Chromatography
Helena Hedlund
CSH Protocols; 2006; doi:10.1101/pdb.prot4199
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Standard Chromatographic Conditions for RP-HPLC of Proteins
C. David Carr and Robert L. Moritz
CSH Protocols; 2006; doi:10.1101/pdb.prot4200
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Separation of Proteins Using Hydrophobic Interaction Chromatography
Richard J. Simpson and Paul A. O’Farrell
CSH Protocols; 2006; doi:10.1101/pdb.prot4201
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Lectin-Agarose Affinity Chromatography
Keith Brocklehurst, Albert J. Courey, Sheraz Gul, Sue-Hwa Lin, and Robert L. Moritz
CSH Protocols; 2006; doi:10.1101/pdb.prot4202
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Protein Ligand Affinity Chromatography
Keith Brocklehurst, Albert J. Courey, Sheraz Gul, Sue-Hwa Lin, and Robert L. Moritz
CSH Protocols; 2006; doi:10.1101/pdb.prot4203
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Directed Orientation of Antibodies during Preparation of Antibody Affinity Resin
Keith Brocklehurst, Albert J. Courey, Sheraz Gul, Sue-Hwa Lin, and Robert L. Moritz
CSH Protocols; 2006; doi:10.1101/pdb.prot4204
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Preparation of DNA Affinity Resin
Keith Brocklehurst, Albert J. Courey, Sheraz Gul, Sue-Hwa Lin, and Robert L. Moritz
CSH Protocols; 2006; doi:10.1101/pdb.prot4205
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DNA Affinity Chromatography
Keith Brocklehurst, Albert J. Courey, Sheraz Gul, Sue-Hwa Lin, and Robert L. Moritz
CSH Protocols; 2006; doi:10.1101/pdb.prot4206
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Preparation of Affinity-Ligand Resins by Immobilization of Dyes on Polyhydroxyl Matrices Using a Direct Coupling Method
Nikos E. Labrou
CSH Protocols; 2006; doi:10.1101/pdb.prot4207
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Preparation of Affinity-Ligand Resins by Immobilization of Dyes on Polyhydroxyl Matrices Using a Spacer Arm
Nikos E. Labrou
CSH Protocols; 2006; doi:10.1101/pdb.prot4208
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Screening Immobilized Dyes for their Ability to Bind a Target Protein
Nikos E. Labrou
CSH Protocols; 2006; doi:10.1101/pdb.prot4209
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Optimization of Adsorption Conditions for Dye-Ligand Affinity Chromatography
Nikos E. Labrou
CSH Protocols; 2006; doi:10.1101/pdb.prot4210
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Optimization of Elution Conditions for Dye-Ligand Affinity Chromatography
Nikos E. Labrou
CSH Protocols; 2006; doi:10.1101/pdb.prot4211
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A Batch Test Tube Method for the Calculation of an Adsorbent’s Available Capacity
Nikos E. Labrou
CSH Protocols; 2006; doi:10.1101/pdb.prot4212
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Purification of Protein Using Dye-Ligand Affinity Chromatography
Nikos E. Labrou
CSH Protocols; 2006; doi:10.1101/pdb.prot4213
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Preparation of a Prepacked IMAC Column
Lars Haneskog
CSH Protocols; 2006; doi:10.1101/pdb.prot4214
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Packing an IMAC Column
Lars Haneskog
CSH Protocols; 2006; doi:10.1101/pdb.prot4215
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Preparation of Clarified E. coli Extract Containing Histidine-Tagged Proteins
Lars Haneskog
CSH Protocols; 2006; doi:10.1101/pdb.prot4216
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Purification of Histidine-Tagged Proteins Using IMAC Without Parameter Optimization
Lars Haneskog
CSH Protocols; 2006; doi:10.1101/pdb.prot4217
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Purification of Histidine-Tagged Proteins under Denaturing Conditions Using IMAC
Lars Haneskog
CSH Protocols; 2006; doi:10.1101/pdb.prot4221
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Chromatography Using a Crystalline Powder Form of Hydroxyapatite
Richard J. Simpson
CSH Protocols; 2006; doi:10.1101/pdb.prot4222
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Extraction and Solubilization of Total Protein from Microorganisms
Angelika Görg, Oliver Drews, and Walter Weiss
CSH Protocols; 2006; doi:10.1101/pdb.prot4224
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Extraction and Solubilization of Total Protein from Plant Seeds
Angelika Görg, Oliver Drews, and Walter Weiss
CSH Protocols; 2006; doi:10.1101/pdb.prot4225
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Extraction and Solubilization of Total Protein from Mammalian Tissue Samples
Angelika Görg, Oliver Drews, and Walter Weiss
CSH Protocols; 2006; doi:10.1101/pdb.prot4226
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Extraction and Solubilization of Mouse Liver Proteins Enriched for Alkaline Proteins
Angelika Görg, Oliver Drews, and Walter Weiss
CSH Protocols; 2006; doi:10.1101/pdb.prot4227
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Sequential Extraction of Wheat Seed Proteins
Angelika Görg, Oliver Drews, and Walter Weiss
CSH Protocols; 2006; doi:10.1101/pdb.prot4228
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Prefractionation of Mouse Liver Proteins with Sephadex-Isoelectric Focusing
Angelika Görg, Oliver Drews, and Walter Weiss
CSH Protocols; 2006; doi:10.1101/pdb.prot4229
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Isoelectric Focusing in Immobilized pH Gradient Strips Using the IPGphor Unit: Sample In-Gel Rehydration
Angelika Görg, Oliver Drews, and Walter Weiss
CSH Protocols; 2006; doi:10.1101/pdb.prot4230
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Isoelectric Focusing in Immobilized pH Gradient Strips Using the IPGphor Unit: Sample Cup Loading
Angelika Görg, Oliver Drews, and Walter Weiss
CSH Protocols; 2006; doi:10.1101/pdb.prot4231
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Multiple SDS-PAGE on Vertical Electrophoresis Units
Angelika Görg, Oliver Drews, and Walter Weiss
CSH Protocols; 2006; doi:10.1101/pdb.prot4232
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Fluorescent Difference Gel Electrophoresis
Angelika Görg, Oliver Drews, and Walter Weiss
CSH Protocols; 2006; doi:10.1101/pdb.prot4233
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Fractionation of Human Plasma Proteins for Two-Dimensional Gel Electrophoresis Using a Multicompartment Electrolyzer (MCE)
Ben R. Herbert, Pier Giorgio Righetti, John McCarthy, Jasmine Grinyer, Annalisa Castagna, Matthew Laver, Matthew Durack, Gerard Rummery, Rebecca Harcourt, and Keith L. Williams
CSH Protocols; 2006; doi:10.1101/pdb.prot4234
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Fractionation of Maize Embryo Proteins for Two-Dimensional Gel Electrophoresis Using a Multicompartment Electrolyzer
Ben R. Herbert, Pier Giorgio Righetti, John McCarthy, Jasmine Grinyer, Annalisa Castagna, Matthew Laver, Matthew Durack, Gerard Rummery, Rebecca Harcourt, and Keith L. Williams
CSH Protocols; 2006; doi:10.1101/pdb.prot4235
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Preparation of Polyclonal Antibodies from Plasma or Serum Using the Gradiflow BF400 Instrument
Vicki L. Locke and Theresa M. Thomas
CSH Protocols; 2006; doi:10.1101/pdb.prot4236
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Concentration of Proteins from Tissue Culture Supernatant Using the Gradiflow BF400 Instrument
Vicki L. Locke and Theresa M. Thomas
CSH Protocols; 2006; doi:10.1101/pdb.prot4237
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Albumin Depletion from Plasma Using the Gradiflow BF400 Instrument
Vicki L. Locke and Theresa M. Thomas
CSH Protocols; 2006; doi:10.1101/pdb.prot4238
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Native Isoelectric Focusing Free-flow Electrophoresis (IEF-FFE) Fractionation of Crude Protein Mixtures
Peter J.A. Weber, Gerhard Weber, and Christoph Eckerskorn
CSH Protocols; 2006; doi:10.1101/pdb.prot4239
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Denaturing Isoelectric Focusing Free-Flow Electrophoresis (IEF-FFE) Fractionation of Crude Protein Mixtures
Peter J.A. Weber, Gerhard Weber, and Christoph Eckerskorn
CSH Protocols; 2006; doi:10.1101/pdb.prot4240
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Preparation of Urea and Guanidinium Chloride Stock Solutions for Measuring Denaturant-Induced Unfolding Curves
Gerald R. Grimsley, Beatrice M.P. Huyghues-Despointes, C. Nick Pace, and J. Martin Scholtz
CSH Protocols; 2006; doi:10.1101/pdb.prot4241
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Determining a Urea or Guanidinium Chloride Unfolding Curve
Gerald R. Grimsley, Beatrice M.P. Huyghues-Despointes, C. Nick Pace, and J. Martin Scholtz
CSH Protocols; 2006; doi:10.1101/pdb.prot4242
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Determining a Thermal Unfolding Curve
Gerald R. Grimsley, Beatrice M.P. Huyghues-Despointes, C. Nick Pace, and J. Martin Scholtz
CSH Protocols; 2006; doi:10.1101/pdb.prot4243
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Measuring the Conformational Stability of a Protein by NMR
Gerald R. Grimsley, Beatrice M.P. Huyghues-Despointes, C. Nick Pace, and J. Martin Scholtz
CSH Protocols; 2006; doi:10.1101/pdb.prot4244
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Hydrogen Fluoride Deglycosylation of Glycoproteins
David Oxley, Graeme Currie, and Antony Bacic
CSH Protocols; 2006; doi:10.1101/pdb.prot4245
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Monosaccharide Composition Analysis: Alditol Acetates
David Oxley, Graeme Currie, and Antony Bacic
CSH Protocols; 2006; doi:10.1101/pdb.prot4246
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Monosaccharide Analysis by Methanolysis
David Oxley, Graeme Currie, and Antony Bacic
CSH Protocols; 2006; doi:10.1101/pdb.prot4247
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Monosaccharide Analysis of Phosphorylated Sugars by Methanolysis and Diazomethane Methylation
David Oxley, Graeme Currie, and Antony Bacic
CSH Protocols; 2006; doi:10.1101/pdb.prot4248
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Linkage Analysis Using the NaOH Methylation Method
David Oxley, Graeme Currie, and Antony Bacic
CSH Protocols; 2006; doi:10.1101/pdb.prot4249
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Measuring Protein Concentration by A280 Using a Single-Beam Spectrophotometer
Joint ProteomicS Laboratory (JPSL) of the Ludwig Institute for Cancer Research and Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
CSH Protocols; 2006; doi:10.1101/pdb.prot4250
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Measuring Protein Concentration by A280 Using a Dual-Beam Spectrophotometer
Joint ProteomicS Laboratory (JPSL) of the Ludwig Institute for Cancer Research and Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
CSH Protocols; 2006; doi:10.1101/pdb.prot4251
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Measuring Protein Concentration in the Presence of Nucleic Acids by A280/A260: The Method of Warburg and Christian
Joint ProteomicS Laboratory (JPSL) of the Ludwig Institute for Cancer Research and Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
CSH Protocols; 2006; doi:10.1101/pdb.prot4252
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Estimating Protein Concentration by Dot Blotting of Multiple Samples
Joint ProteomicS Laboratory (JPSL) of the Ludwig Institute for Cancer Research and Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
CSH Protocols; 2006; doi:10.1101/pdb.prot4253
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Rapid Measurement of Protein Concentration by Western Analysis Using Colorimetric Detection by BCIP-NBT
Joint ProteomicS Laboratory (JPSL) of the Ludwig Institute for Cancer Research and Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
CSH Protocols; 2006; doi:10.1101/pdb.prot4254
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