number Protocols

Category: PCR Protocols

The MagneSil system can selectively isolate PCR products that are more than 150-bp long from primers and primer -dimers.  The technology can be used with a number of robotic workstations, including Beckman Coulter’s Biomek 2000 and FX Laboratory Automation Workstations.  The procedure can also be carried out manually.  Typical recovery is more than 80% for a 1-kb product with negligible carryover of primers or nucleotides. - [Read A Magnetic Particle-Based Method for Purifying PCR Products from Solution Protocol]

Category: Reporter Gene Assays: B-Galactosidase Assay Protocols

In the method described here, the cells are permeabilized to allow the substrate to enter the cells and the activity is normalized to the number of cells assayed. - [Read Assay of ß-Galactosidase in Yeast: Permeabilized Cell Assay]

Category: Yeast Protocols: Yeast Genetics Protocols: B-Galactosidase Assay Protocols

In this protocol, the cells are permeabilized to allow the substrate to enter the cells and the activity is normalized to the number of cells assayed. - [Read Assay of ß-Galactosidase in Yeast: Permeabilized Cell Assay Protocol]

Category: Cell Culture Protocols: Sterile Technique Protocols

Cultured mammalian cells are used extensively in cell biology studies; it requires a number of special skills in order to be able to preserve the structure, function, behavior and biology of the cells. This unit describes the basic skills required to maintain and preserve cell cultures: aseptic technique, medium characteristics, passaging, freezing and storage, recovering frozen stocks, and counting viable cells. - [Read Basic Techniques for Mammalian Cell Tissue Culture Protocol]

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

Cultured mammalian cells are used extensively in cell biology studies; it requires a number of special skills in order to be able to preserve the structure, function, behavior and biology of the cells. This unit describes the basic skills required to maintain and preserve cell cultures: aseptic technique, medium characteristics, passaging, freezing and storage, recovering frozen stocks, and counting viable cells. - [Read Basic Techniques for Mammalian Cell Tissue Culture 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: Pharmacology and Toxicology Protocols: Cytotoxicity Protocols

Protocol for CellTiter-Glo luminescent cell viability assay. This assay is a homogeneous method of determining the number of viable cells in culture based on quantitation of the ATP present, which signals the presence of metabolically active cells. - [Read CellTiter-Glo Luminescent Cell Viability Assay Protocol]

Category: Plant Biology Protocols: Arabidopsis Genetics Protocols

Method is for preparing chromosomes from single flower buds of A. thaliana. It does not kill the plants allowing the determination of their chromosome number throughout development. Includes: Preparations of Arabidopsis; Preparation of Chromosome; Staining Chromosomes. - [Read Chromosome Spreads from Flower Buds of Arabidopsis thaliana Protocol]

Category: PCR Protocols: Reverse Transcriptase RT-PCR Protocols

In this protocol, sample and competitor RNAs are reverse transcribed (separately) in a pilot experiment.  A constant amount of sample RT product is then combined with a 2-logserial dilution of competitor RT product for PCR. Procedure provides an approximate copy number for the sample, which is then fine-tuned by repeating the experiment with a series of twofold dilutions of competitor.  The experiment includes controls for sample-to-sample variations in RT efficiency. - [Read Competitive RT-PCR: Estimation of Copy Number Protocol]

Category: Immunology

Protocol for detection of autoantibodies with self-assembling radiolabeled antigen tetramers. Details how to produce radiolabeled antigen-streptavidin tetramers for detection of antibodies by immunoprecipitation. Optionally, the antigen tetramers can be denatured to compare responses to folded and unfolded antigen in the same system. This technique can be applied to a large or small number of samples, and a given sample can be simultaneously assayed with multiple antigens. - [Read Detection of Autoantibodies with Self-Assembling Radiolabeled Antigen Tetramers Protocol]

Category: Cytogenetics Protocols: In Situ Hybridization Tissue Sections Protocols

Protocol for detection of even-skipped transcripts in drosophila embryos with PCR/DIG-labeled DNA probes. This protocol has been used to detect the transcript distribution of a number of genes by in situ hybridization, including evenskipped and seven-up, in whole mount Drosophila embryos, and engrailed Antennapedia in whole mount grasshopper embryos. Includes: Probe labeling; Evaluation of labeling reaction; Preparation of embryos, hybridization and detection.
 - [Read Detection of Even-Skipped Transcripts in Drosophila Embryos with PCR/DIG-Labeled DNA Probes Protocol]

Category: Fungi Protocols: Fungi Genetics Protocols

Standard operating procedure for the determination of tissue fungal burden utilizing quantitative real time polymerase chain reaction (QPCR). This standard operating procedure will provide information on how to assess fungal tissue burden of infected animals by use of a single copy (FKS) or multicopy gene (18s RNA) to assess the number of fungal cell nuclei present. - [Read Determination of Tissue Fungal Burden Utilizing Quantitative Real Time Polymerase Chain Reaction]

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: Plant Biology Protocols: Arabidopsis Genetics Protocols

EMS is used at concentrations that induce multiple point mutations in each plant, such that mutant alleles of a specific locus are found at a rate of ~1 in 2000-5000 M2 plants. This high rate of mutagenesis makes possible the screening of relatively few plants to find those with the phenotype of interest, a particular advantage if the screen is laborious or if only a small number of genes mutate to the required phenotype. - [Read EMS Mutagenesis of Arabidopsis Seed Protocol]

Category: Cell Biology and Cell Culture: Flow Cytometry Protocols

Protocol for estimating the number of CD38 molecules on the CD8+ T lymphocytes of HIV-infected individuals. Includes: RECOMMENDATION OF VENDOR FOR PE-CD38 AND PE-CD4; VALIDATION OF LOGARITHMIC AMPLIFIER LINEARITY AND SENSITIVITY; CONSERVATION OF THE LEVEL OF CD4 ANTIGEN EXPRESSION ON CD4+ LYMPHOCYTES AND ITS USE AS A BIOLOGIC STANDARD FOR FLOW CYTOMETER INSTRUMENT CHARACTERIZATION; DETERMINATION OF THE NUMBER OF CD38 MOLECULES PER CD8+ CELL; etc.. - [Read Estimating the Number of CD38 Molecules on the CD8+ T Lymphocytes of HIV-Infected Individuals]

Category: Cell Culture Protocols

Protocol describes a method for estimation of mammalian cell number in a defined volume of medium using a hemocytometer. Automated methods using cell-counting devices such as those produced by Coulter are desirable when large numbers of individual samples are to be counted. - [Read Estimation of Cell Number by Hemocytometry Counting Protocol]

Category: PCR Protocols: cDNA Synthesis Protocols

This cDNA synthesis system simplifies your work dramatically.  All reaction components are premixed and lyophylised.  You have to add your RNA and (for Your-Prime beads) the primer.  Another advantage of the system is a little number of pipetting steps required, and therefore reduced risk of Rnase contamination and RNA degradation. - [Read First strand cDNA synthesis with Ready-To-Go Beads Protocol]

Category: Cell Organelle Protocols: Subcellular Fractionation Protocols

A number of density gradient strategies have been developed for the fractionation of human erythrocytes according to their age. As the cells age, so their density tends to increase; reticulocytes therefore tend to have the lowest densities. Reticulocytes have frequently been partially purified on discontinuous gradients of arabinogalactan; the actual density range being quite varied, from quite broad ones. - [Read Fractionation of Human Erythrocytes (Normal or Sickle) and Reticulocytes in Discontinuous Iodixanol]

Category: Stem Cell Protocols

This protocol describes a method for freezing and thawing ES cells using cryovials. It is important to freeze ES cell stocks as soon as possible to reduce the time that they are in culture. A careful record should be kept of the number of times cells are passaged and the location of the cryovials. - [Read Freezing and Thawing of Embryonic Stem (ES) Cells Using Cryovials Protocol]

Category: Cell Culture Protocols: Cell Immortalization Protocols

Cultivating animal cells in the laboratory is an indispensable technique for cell biologists. However, most normal primary cell lines, while faithfully reproducing the phenotype of their tissue of origin, do not grow indefinitely in culture. After a series of population doublings (the number of which varies by species, cell type, and culture conditions) primary cells enter a state where they no longer divide. - [Read Immortalization of Cells in Culture]

Category: Immunology: Immunofluorescence Protocols: Immunofluorescence Staining Protocols

Protocol for immunostaining of DDR proteins in senescent cells. Detailed methodology to study the activation of a number of DNA damage response factors in senescent human fibroblasts. - [Read Immunostaining of DDR Proteins in Senescent Cells Protocol]

Category: Viral Manipulation Protocols: Phage Lamda Manipulation Protocols

Pilot ligations and packaging reactions are used to establish the amounts of fragmented genomic DNA and bacteriophage {lambda} arms that yield the maximum number of recombinants. Additional ligation and packaging reactions may then be set up to yield a comprehensive library of genomic DNA. - [Read Ligation of Bacteriophage lambda Arms to Fragments of Foreign Genomic DNA Protocol]

Category: Viral Culture and Isolation Protocols: Viral Culture Protocols

5 ml liquid lysates are prepared when a small amount of DNA from a large number of lambda clones is needed. The lysates can be made using 10- 20 ul of a stock lysate or a 100-fold amplified phage "macroplaque" as the inoculum. - [Read Liquid Phage Lysates Protocol]

Category: Immunology: B Cell Protocols

This assay is used to measure cell viability. It is a two-color fluorescence assay that simultaneously determines: Live cell number and Dead cell number. - [Read Live Dead Assay for Cell Viability Protocol]

Category: Cell Biology and Cell Culture: Cell Viability Protocols

Assay measures cell viability. It is a two-color fluorescence assay that simultaneously determines Live cell number and Dead cell number. This protocol is designed for use with the GEMINI XS Microplate Spectrofluorometer, a multi-well plate scanner with dual excitation/emission capabilities, but the assay is also adaptable for flow cytometry and fluorescence microscopy. Includes: Cell Culture; Preparation for the Assay; Live/Dead Assay; Reading the Plate; Data Analysis; Alternative protocol. - [Read Live/Dead Assay for Cell Viability Protoco]