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(LCM): Preparation and Sectioning of Frozen Tissue Blocks and Purification of RNA from Isolated Cel - http://www.cshprotocols.org/cgi/content/extract/2006/1/pdb.prot4107

Category: Primary Cell Isolation and Culture Protocols: Laser Capture Microdissection Protocols: Tissue Preparation for LCM Protocols

LCM isolates specific cells or tissues from samples mounted on microscope slides. The samples are viewed through a thermoplastic film that is attached to a microcentrifuge tube lid. Localized heat, caused by the application of a laser pulse, fuses the membrane to the cells of interest, which can then be harvested for further analysis. RNA and proteins can be purified from the isolated cells, allowing detailed analysis of gene expression. This protocol is divided into three stages. - [Read (LCM): Preparation and Sectioning of Frozen Tissue Blocks and Purification of RNA from Isolated Cel]

A Batch Test Tube Method for the Calculation of an Adsorbent’s Available Capacity Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/1/pdb.prot4212

Category: Chromatography Protocols: Affinity Chromatography Protocols

Protocol describes a batch test tube method for the calculation of an adsorbent’s available capacity. - [Read A Batch Test Tube Method for the Calculation of an Adsorbent’s Available Capacity Protocol]

An Image-Based Assay of Endothelial Cell Tube Formation - http://www.bdbiosciences.com/pdfs/whitePapers/06-A790030-3A1.pdf

Category: Signalling Signal Transduction Protocols

Protocol on an image-based assay of endothelial cell tube formation as a model of angiogenesis. Includes: Introduction, Methods, Results, Discussion and References. - [Read An Image-Based Assay of Endothelial Cell Tube Formation]

An Image-Based Assay of Endothelial Cell Tube Formation as a Model of Angiogenesis - http://www.bdbiosciences.com/pdfs/whitePapers/06-A790030-3A1.pdf

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]

Calibration of Becton Dickinson Flow Cytometers for Relative Fluorescence Intensity Measurements - http://cyto.mednet.ucla.edu/Protocols/relative.htm

Category: Cell Biology and Cell Culture: Flow Cytometry Protocols: Flow Cytometry Calibration Protocols

Flow cytometers must be calibrated prior to fluorescence intensity measurements because of inherent instrument variability. To correct for this variability, a standard particle (fixed chicken red blood cells, or CRBCs) must be analyzed on the instrument prior to each experiment and photomultiplier tube (PMT) voltages adjusted accordingly to place the CRBC fluorescence emission peaks into predetermined target channels. - [Read Calibration of Becton Dickinson Flow Cytometers for Relative Fluorescence Intensity Measurements]

Centrifuge Tube Chemical Resistance Chart - http://www.bdbiosciences.com/discovery_labware/technical_resources/labtools/p38.pdf

Category: General Research Protocols and Methods: Centrifuge Use and Centrifugation

Centrifuge Tube Chemical Resistance Chart. Polypropylene, polystyrene. PS, PP. BD Biosciences. - [Read Centrifuge Tube Chemical Resistance Chart]

Concentration of Oligo DNA by Ethanol Precipitation Protocol - http://mycoplasmas.vm.iastate.edu/lab_site/methods/DNA/precip.html

Category: Oligonucleotide Protocols: Oligonucleotide Purification Protocols

Concentration of DNA by Ethanol Precipitation Protocol. Adapted from Bruce A. Roe, Department of Chemistry and Biochemistry, The University of Oklahoma, Norman, Oklahoma. Usually 2.5 - 3 volumes of ethanol and/or acetate solution is added to the DNA in a microcentrifuge tube. This is then put into an ice-water bath for at least 10 minutes. The precipitation is performed by incubation at -20C overnight. - [Read Concentration of Oligo DNA by Ethanol Precipitation Protocol]

DNA Extraction from Cheek Cells - http://geneticslab.topcities.com/cheekcells.htm

Category: DNA Protocols: DNA Extraction Protocols

Cheek cells obtained by rinsing the mouth commercial mouth wash solution. Mouth wash is then discarded into a sterile conical tube and sent to the lab. Based on Salting out procedure. DNA Laboratory, Medical School, Malta. - [Read DNA Extraction from Cheek Cells]

Image Based Assay of Endothelial Cell Tube Formation Protocol - http://www.bdbiosciences.com/pdfs/whitePapers/06-A790030-3A1.pdf

Category: Pharmacology and Toxicology Protocols: Drug Discovery

Protocol describes an assay that relies 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. Although quantification of the tubules can be performed by manual tracing, this method precludes the use of the assay in unbiased high-throughput applications. - [Read Image Based Assay of Endothelial Cell Tube Formation Protocol]

Lipoplex and LPD Nanoparticles for In Vivo Gene Delivery Protocol - http://www.cshprotocols.org/cgi/content/abstract/2006/1/pdb.prot4448

Category: Gene Delivery Protocols: DNA Nanoparticles Protocols

Lipoplex (cationic liposome-DNA complex) is formed via electrostatic interaction of anionic nucleic acids with cationic liposomes. A thin film of lipids is dried on the bottom of a glass tube and rehydrated in an aqueous solution. The resulting liposome suspension is passed through polycarbonate filters of desired pore size. This protocol also describes the preparation, physical properties, and biological activity of liposome-polycation-DNA (LPD) nanoparticles. - [Read Lipoplex and LPD Nanoparticles for In Vivo Gene Delivery Protocol]

Maintenance of Stocks of Marine Hypotrichs Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/21/pdb.prot4469

Category: Laboratory Model Organisms Protocols

Protocol describes the preparation of stocks of marine hypotrichs for long-term storage. Marine euplotids are maintained by serial passage of tube stocks. - [Read Maintenance of Stocks of Marine Hypotrichs Protocol]

Method to Analyze Meiotic Segregation Patterns in Coprinus cinereus Using PCR - http://www.fgsc.net/fgn/freedman.html

Category: Fungi Protocols: Fungi Genetics Protocols

Quick and reliable method to analyze meiotic segregation patterns in Coprinus cinereus using the polymerase chain reaction. The advantages of this method include: 1. The tissue is grown and lyophilized in the same tube, which facilitates the simultaneous analysis of many segregants. 2. Only one extraction step is necessary. 3. The markers are scored by gel electrophoresis, thereby bypassing Southern analysis. - [Read Method to Analyze Meiotic Segregation Patterns in Coprinus cinereus Using PCR]

Multiplex Real-Time PCR Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/1/pdb.prot4113

Category: PCR Protocols: Real-Time PCR Protocols

In multiplex real-time PCR, different sets of primers with different labels are used to amplify separate genes from the template DNA in one tube. This protocol uses LUX (Light Upon eXtension) primers from invitrogen. FAM (6-carboxy-fluorescein) is used to label the gene of interest, and JOE (6-carboxy-4', 5'-dichloro-2',7'-dimethoxy-fluorescein) is used to label a housekeeping gene as an internal control to normalize between different reactions. - [Read Multiplex Real-Time PCR Protocol]

Nematode Dye Filling Protocol - http://www.k-state.edu/hermanlab/protocols/nematode_dye_filling.htm

Category: C. elegans Protocols: C. elegans Staining Protocols

Protocol for nematode dye filling. Includes: Thumb plate; Microfuge tube; 15 ml tube; Viewing: Big Scope and Dissecting Scope. - [Read Nematode Dye Filling Protocol]

One-Step Isolation of Plant DNA Suitable for PCR Amplification - http://pubs.nrc-cnrc.gc.ca/ispmb/ispmb19/r01-054.pdf

Category: Plant Biology Protocols: Plant DNA RNA Isolation Protocols

One step extraction for isolation of plant DNA. DNA suitable for amplification by PCR can be produced from leaf material smaller than 0.3 mm2 in less than 20 min & no tube changes. Method was tested on several plant species. Method was found to extract DNA that could be amplified without any further purification or treatment. The isolated DNA was amplified using a universal chloroplast primer set. The method was validated by comparing size of PCR products generated using standard DNA isolation. - [Read One-Step Isolation of Plant DNA Suitable for PCR Amplification]

Rapid and Efficient Site-directed Mutagenesis by the Single-tube Megaprimer PCR Method Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/2/pdb.prot3467

Category: Cloning Protocols: Mutagenesis Protocols

Protocol for rapid and efficient site-directed mutagenesis by the single-tube megaprimer PCR method. - [Read Rapid and Efficient Site-directed Mutagenesis by the Single-tube Megaprimer PCR Method Protocol]

Selection of an Ion Exchanger Protocol III - http://cshprotocols.cshlp.org/cgi/content/extract/2006/1/pdb.prot4193

Category: Chromatography Protocols: Ion Exchange Chromatography Protocols

Protocol for selection of an ion exchanger: Determining the pI of a protein using the test tube method. The choice of whether to use an anion or a cation exchanger should be based on knowledge of the stability of the protein, and the binding properties of the target protein and other molecules present in the sample. - [Read Selection of an Ion Exchanger Protocol III]

Single tube confirmation PCR protocol - http://www-sequence.stanford.edu/group/yeast_deletion_project/single_tube_protocol.html

Category: DNA Protocols: PCR Polymerase Chain Reaction Protocols

Single tube confirmation PCR protocol. Saccharomyces Genome Deletion Project. - [Read Single tube confirmation PCR protocol]

Single tube confirmation PCR protocol - http://www-sequence.stanford.edu/group/yeast_deletion_project/single_tube_protocol.html

Category: PCR Protocols

Single tube confirmation PCR protocol. Saccharomyces Genome Deletion Project. - [Read Single tube confirmation PCR protocol]

Single tube confirmation PCR protocol - http://www-sequence.stanford.edu/group/yeast_deletion_project/single_tube_protocol.html

Category: PCR Protocols: Colony PCR

The following colony PCR protocol has been designed to be performed in individual reaction tubes. We usually test three colonies from each transformation along with a wild-type control. A series of five different PCR tests are performed on each colony to - [Read Single tube confirmation PCR protocol]

Single Tube Confirmation Yeast PCR Protocol - http://sequence-www.stanford.edu/group/yeast_deletion_project/single_tube_protocol.html

Category: Yeast Protocols: Yeast Nucleic Acid Protocols: Yeast PCR Protocols

Protocol for single tube confirmation yeast PCR. Includes: Clonal purification; Zymolyase treatment; PCR reactions; PCR conditions; Agarose gel electrophoresis. - [Read Single Tube Confirmation Yeast PCR Protocol]

Single-tube Coupled Transcription/Translation Reactions for Eukaryotic In Vitro - http://www.promega.com/tbs/tm045/tm045.pdf

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

Information for protocol using single-tube, coupled transcription/translation reactions for eukaryotic in vitro translation. Includes information on: Translation Procedure; Positive Control Translation Reactions Using Luciferase; Cotranslational Processing Using Canine Pancreatic Microsomal Membranes; Post-Translational Analysis; Positive Control Luciferase Assays; Composition of Buffers and Solutions; Luciferase SP6/T7 Control DNAs - [Read Single-tube Coupled Transcription/Translation Reactions for Eukaryotic In Vitro]

Subfractionation of Low-Density Lipoprotein (LDL) - http://www.axis-shield.com/densityhome/optiprep/M11.pdf

Category: Cell Organelle Protocols: Subcellular Fractionation Protocols

In the routine method described in this protocol, chylomicron-free plasma is adjusted to 12% (w/v) iodixanol and the sample, essentially fills an approx 3 ml tube for a near-vertical rotor. During the centrifugation VLDL, LDL and HDL particles and also plasma proteins migrate from all parts of the sample to their final buoyant density banding position in the self-forming density gradient. - [Read Subfractionation of Low-Density Lipoprotein (LDL)]

Articles (1-10 of 14)

Populational Analysis of Genomic DNA Protocol

A protocol on the populational Analysis of genomic DNA.

Lambda Phage Protocol Large DNA Preparation

Single Stranded Plasmid DNA Isolation Protocol

A Single Stranded Plasmid DNA Isolation Protocol describing the production and isolation of single-stranded DNA (ssDNA) using bacteriophagemid-containing bacteria and helper phage. Infection of the host cells with helper phage allows for packaging of ssDNA into bacteriophage. The ssDNA can then be isolated from phage particles.

Genomic DNA Labeling of Microarrays Protocol

DNA microarrays are an ordered arrangement of DNA molecules complementary to genes of interest that are "spotted" by robotic equipment onto a glass slide substrate. The expression of genes in cells can be monitored with microarrays by preparing cDNA from the mRNA of cells of interest and measuring the hybridization to the microarray. This protocol describes the labeling of genomic DNA for use as a probe for hybridization to the cDNA spotted on the array.

Drosophila Cell Transfection Protocol

A simple Drosophila tissue culture cell transfection method.

Tubulin Polymerization Protocol using GTP and GMPCPP

Tubulin is polymerized into microtubules by incubating tubulin at 37°C with GTP. A nucleation seed is added when the purpose is to assay microtubule elongation. Tubulin can also be polymerized for the purposes of recycling the tubulin or labeling the microtubules with fluorescently labeled tubulin. Based on the protocol by Timothy Mitchison of Harvard University.

Microarray Protocol Preparation of Fluorescent DNA Probes from Human mRNA

This Microarray Protocol Preparation of Fluorescent DNA Probes from Human mRNA protocol describes the production of probes labeled with the fluorescent dyes, Cy3 and Cy5, following the synthesis of cDNA from human mRNA and the hybridization of the probes to DNA microarrays.

Acid Guanidinium Thiocyanate RNA Isolation Phenol Chloroform Extraction

A single step RNA isolation protocol using Phenol Chloroform Extraction and Acid Guanidinium Thiocyanate. This RNA isolation method uses the fact that guanidinium thiocyanate can simultaneously lyse the cells and inactive cellular RNAses during the initial RNA isolation step allow a single step in the method.

In Vitro Translated Xenopus Mos Kinase Assay Protocol

In Vitro Translated Xenopus Mos Kinase Assay Protocol. In response to progesterone, immature Xenopus oocytes mature to eggs that can be fertilized. The Mos protein kinase is essential for oocyte maturation, most likely due to its ability to activate the MAP kinase cascade. This MAP kinase cascade eventually leads to the activation of Cdc2/cyclin B and entry into M phase. In this protocol, tagged Mos kinase is translated in vitro, immunopurified, and used in a kinase assay.

Immobilized Antigen Phage Antibody Selection Protocol

A protocol for the selection of Phage Antibodies using Immobilized Antigen. This method describes the selection of antibodies from bacteriophage antibody libraries that recognize a specific antigen. The phage display library of antibody-displaying phage particles is exposed to antigen attached to a solid substrate (Nunc Immuno™ tubes). The phage particles with affinity for antigen bind to the immobilized antigen and are selected from the library of phage expressing antibodies.

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