assays Protocols

Category: Protein Protocols: Nuclear Extraction Protocols

Nuclear Extract protocol is optimized for about 10^7 cells, can use for gel shift assays and western blotting. Mirmira Lab, Univ. Virginia - [Read Preparation of Nuclear Extracts for Gel Shifts and Westerns Blots]

Category: DNA Protocols: Chromatin Immunoprecipitation Protocols

Formaldehyde cross-linking and chromatin immunoprecipitation assays of tissue culture cells, Based on Boyd and Farnham. Michelle Kallesen, Rosen Lab. - [Read ChIP Assay Protocol PDF]

Category: ELISA Protocols: Sandwich ELISA Assay Protocols

Sandwich ELISA Protocol. Chemicon. General Protocol for the Sandwich ELISA method, Troubleshooting Sandiwich ELISA Assays. - [Read Sandwich ELISA Protocol]

Category: Protein Protocols: Protein Precipitation Procols

A protein precipitation procedure used to precipitate protein from cell lysates. Allows for optimal protein recovery and accurate assays. The Signaling Gateway - [Read TCA/Acetone Precipitation (Large Scale) PDF]

Category: RNA Protocols: RNA-binding Protein EMSA Interactions

SULLY et al., 2004 Biochem. J. 377 (629–639). - [Read RNA EMSA (electrophoretic mobility shift assays) and UV cross-linking]

Category: Protein Protocols: Protein Extraction From Tissue

Plant Protein Isolation - Rapid isolation of protein for SDS-PAGE analysis. (Essentially the same protocol as that described for GUS Assays). Stockinger Lab - [Read Plant Protein Isolation]

Category: Protein Protocols: Lowry Protein Assay

Lowry Protein Assay. The Lowry procedure is one of the most venerable and widely-used protein assays, being first described in 1951 [Lowry et al., J. Biol. Chem. 193: 265-275 (1951)]. Under alkaline conditions, copper complexes with protein. When folin phenol reagent (phospho-molybdic-phosphotungstic reagent) is added, the Folin-phenol reagent binds to the protein. Bound reagent is slowly reduced and changes color from yellow to blue. P.J. Hansen, Dept. of Animal Sciences, University of Florida. - [Read Lowry Protein Assay]

Category: Protein Protocols: Protein Purification and Identification

Protein Purification: Assays, Specific Activity, Initial Fractionation. Blaber Lecture. - [Read Protein Purification: Assays, Specific Activity, Initial Fractionation]

Category: Antibody Protocols: Antibody Production Protocols

Protocol for polyclonal antibody production. Very useful for rapid and simple generation of antibodies for western blots, ELISA assays, and immunoprecipitation. Includes: Rabbit Immunization; Initial Preparation; Pre-bleed; Antigen Injection; Monitoring of Titer; Purification of Antibodies. - [Read Polyclonal Antibody Production Protocol]

Category: Protein Protocols: Protein Quantitation Concentration Protocols

Absorbance assays are fast and convenient, since no additional reagents or incubations are required.  No protein standard need be prepared.  The assay does not consume the protein.  The relationship of absorbance to protein concentration is linear.  Because different proteins and nucleic acids have widely varying absorption characteristics there may be considerable error, especially for unknowns or protein mixtures. - [Read Absorbance Assay 280 nm]

Category: Primary Cell Isolation and Culture Protocols: Mammalian Cell Culture Protocols

Cryopreserved PBMCs are a common specimen source for studies of immunological responses to vaccines, immunotherapies, etc. The health and viability of cells recovered post-cryopreservation are of course critical to the success and accuracy of immunological assays performed on them. This protocol standardizes PBMC isolation and cryopreservation techniques, specifically for the assessment of thawed cells by cytokine flow cytometry. - [Read Protocol for Isolation, Cryopreservation, and Thawing of PBMCs]

Category: Immunology: Chemotaxis

MONOCYTE AND NEUTROPHIL ISOLATION. The protocol describes the method used for isolation of monocytes and neutrophils used in both the chemotaxis assay and microbicidal assays. Pediatric AIDS Clinical Trials Group - [Read MONOCYTE AND NEUTROPHIL ISOLATION]

Category: Protein Protocols: Protein Ubiquitination Protocols

A specific endpoint assay for ubiquitin. Rose et al., Proc Natl Acad Sci U S A. 1987. Simple endpoint assays for free ubiquitin (Ub) and for the Ub-activating enzyme are described. . - [Read A specific endpoint assay for ubiquitin.]

Category: Cell Biology and Cell Culture: Flow Cytometry Protocols: Cell Cycle Analysis Protocols

Describes assays used to determine the distribution of a population of cells to the different stages of the cell cycle as analyzed by flow cytometry. Staining the DNA with different fluorescent dyes, propidium iodide or DAPI, is one of the most direct ways of staging the cells based on DNA content. - [Read Determining Cell Cycle Stages by Flow Cytometry Protocol]

Category: Cell Biology and Cell Culture: Cell Viability Protocols

Cell-based assays are important tools for contemporary biology and drug discovery because of their predictive potential for in vivo applications.This assay gives ratiometric, inversely proportional values of viability and cytotoxicity (Figure 4.15) that are useful for normalizing data to cell number. Also, this reagent is compatible with additional fluorescent and luminescent chemistries. - [Read Determining Number of Live and Dead Cells in Cell Population: Cytotoxicity Assay Protocol]

Category: Cell Biology and Cell Culture: Endothelial Cell Protocols

Traditional animal models to quantify the degree of blood vessel formation are being replaced by cell culture assays that are easier to set up, statistically reliable and can be automated in a drug screening laboratory. These assays rely on the endothelial cells’ ability to form distinct blood-vessel-like tubules in an extracellular matrix where they can subsequently be visualized by fluorescence microscopy. - [Read An Image-Based Assay of Endothelial Cell Tube Formation as a Model of Angiogenesis]

Category: Cell Biology and Cell Culture: In Vitro Reconstitution Protocols

Protocol includes procedure for Transwell in vitro migration assays. - [Read Protocol for Trans-Well Migration Assay]

Category: Reporter Gene Assays: B-Galactosidase Assay Protocols

There are two basic methods for the in vitro assay of B-galactosidase activity from yeast. They differ mainly in the method of preparing the material for assay. Both methods are described with accompanying protocols. Method I: Assay of Crude Extracts includes: Yeast Cell Growth; Yeast Cell Harvest; B-gal assays; Bradford Assays. Method II: Permeabilized cell assay. - [Read Assay of β-Galactosidase in Yeast Protocol]

Category: Cell Biology and Cell Culture: Cell Viability Protocols

The CellTiter-Glo® Luminescent Cell Viability Assay is a homogeneous method to determine the number of viable cells in culture. Detection is based on using the luciferase reaction to measure the amount of ATP from viable cells. The amount of ATP in cells correlates with cell viability. - [Read Cell Viability Assays that Measure ATP Protocol]

Category: Cell Biology and Cell Culture: Cell Viability Protocols

Protocol and methods on assays to detect apoptosis. - [Read Assays to Detect Apoptosis Protocol]

Category: Molecular Biology Protocols: Carbohydrate Protocols

o determine the relative amounts of LPS carbohydrates present in a given strain. The assay can be done on one set of samples and then scanned at the various wavelengths for reasonable data on the 3 types of sugars. HEXOSE ASSAY, 6-DEOXYHEXOSE ASSAY, HEPTOSE ASSAY. Hancock Laboratory. - [Read Carbohydrate Assays]

Category: Immunology: T Cell Protocols

Protocols describe the conditions required to induce proliferation are described. Also describe the assay in which CD4·CD25·T cells are co-cultured with conventional T cells in order to assess their suppressive function. Will describe the culture conditions for the activation and expansion of CD4·CD25· cells. - [Read Proliferative Assays for T Cell Function Protocols]

Category: Cell Biology and Cell Culture: Cell Viability Protocols

Choosing a cell viability or cytotoxicity assay from among the many different options available can be a challenging task. Includes information on: Establishing an In Vitro Model System; Choosing an Endpoint to Measure; Characterizing Assay Responsiveness; Determining Dose and Duration of Exposure; Homogeneous Assays for Multiwell Formats and Automated Screening; Additional Factors to Consider When Choosing a Cell Viability Assay; Cell Viability Assays that Measure ATP Protocol; etc.. - [Read Cell Viability Information For Protocols and Applications]

Category: Cell Biology and Cell Culture: In Vitro Reconstitution Protocols

The ability to synthesize RNA in the lab is critical to many techniques.Radiolabeled and nonisotopically labeled RNA probes, generated in small scale transcription reactions can be used in blot hybridizations and nuclease protection assays. This article includes information on: Requirements For Transcription, RNA Phage Polymerases, Template Options: Plasmids, PCR Products, Oligonuclotides and cDNA, Sense or Antisense, Conventional Or Large Scale Synthesis, Products for In Vitro Transcription. - [Read Basic Information on In Vitro Transcription]

Category: Reporter Gene Assays

Protocol for GUS reporter gene assay. Includes: Protein isolation; Alternative method for small (<1g) quantities of tissue; GUS assays; Bradford protein concentration determination assays - [Read GUS Reporter Gene Assay Protocol]