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3-7 Assay Protocol - http://www.promega.com/tbs/tb323/tb323.pdf

Category: Pharmacology and Toxicology Protocols: Enzyme Assays Protocols

Protocol for 3/7 assay. Includes: Detection of Caspase-3 and -7 Activities in Cell-Based Assays; Detection of Caspase-3 or -7 Activity Using Purified Caspases. - [Read 3-7 Assay Protocol]

5-Bromo-2-Deoxyuridine (BrdU) and 7-Amino-Actinomycin (7-AAD) Staining for Cell Proliferation Assay - http://www.natureprotocols.com/2007/01/22/5bromo2deoxyuridine_brdu_and_7.php

Category: Cell Biology and Cell Culture: Flow Cytometry Protocols: DNA Staining Protocols for Flow Cytometry

The incorporation of 5-bromo-2-deoxyuridine (BrdU) in replicating DNA of proliferating cells can be used to measure their proliferation. This protocol allows the identification of cells which have incorporated BrdU by flow cytometry. - [Read 5-Bromo-2-Deoxyuridine (BrdU) and 7-Amino-Actinomycin (7-AAD) Staining for Cell Proliferation Assay]

96-well RNA In Situ Hybridization Protocol - http://www.fruitfly.org/about/methods/RNAinsitu.html

Category: PCR Protocols: In-situ PCR Protocols

96-well RNA In Situ Hybridization Protocol. Probe Preparation, Cell Inoculation, PCR, RNA Probe Preparation, etc, Very In-depth Protocol and Method Conditions. Berkeley Drosophila Genome Project. - [Read 96-well RNA In Situ Hybridization Protocol]

A Sealed Preparation for Long-Term Observations of Cultured Cells - http://www.cshprotocols.org/cgi/content/abstract/2007/1/pdb.prot4660

Category: Microscopy Protocols: Live-Cell Imaging Protocols

This protocol describes a sealed preparation that allows the continuous long-term observation of cultured mammalian cells on upright or inverted microscopes without environmental CO2 control. The preparation allows for optical conditions consistent with high-quality imaging and good cell viability for at least 100 hours. - [Read A Sealed Preparation for Long-Term Observations of Cultured Cells]

A simple method for estimating global DNA methylation using bisulfite PCR of repetitive DNA elements - http://nar.oxfordjournals.org/cgi/content/full/32/3/e38

Category: Epigenetics and Methylation Protocols: Bisulfite Treatment Methylation Assay Protocol

Yang et al, NAR. 2004. ue to the heavy methylation of repetitive elements, this assay was especially useful in detecting decreases in DNA methylation, and this assay was validated by examining cell lines treated with the methylation inhibitor 5-aza-2'deox - [Read A simple method for estimating global DNA methylation using bisulfite PCR of repetitive DNA elements]

A Single-step Method for the Simultaneous Preparation of DNA, RNA, and Protein from Cells and Tissue - http://www.cshprotocols.org/cgi/content/extract/2006/2/pdb.prot4056

Category: Nucleic Acid Purification Protocols

Protocol for a single-step method for the simultaneous preparation of DNA, RNA, and protein from cells and tissues. The yield of total RNA depends on the tissue or cell source, but it is generally in the range of 4-7 µg/mg starting tissue or 5-10 µg/106 cells. IMPORTANT: Prepare all reagents used in this protocol with Diethyl pyrocarbonate (DEPC)-treated H2O. - [Read A Single-step Method for the Simultaneous Preparation of DNA, RNA, and Protein from Cells and Tissue]

AA & Metabolite Quantitation of Cell Pellets Post-AA Labeling Protocol - http://www.duke.edu/web/ceramide/protocols/0024.html

Category: Lipid Protocols: Arachidonic Acid Protocols

Protocol for AA and metabolite quantitation of cell pellets post AA labeling. Includes: Extraction and TLC. - [Read AA & Metabolite Quantitation of Cell Pellets Post-AA Labeling Protocol]

Adapting Cells to a Serum-Free Environment Protocol - https://fscimage.fishersci.com/webimages_FSC/downloads/HyClone_Protocol_8.pdf

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

There are many ways to adapt cell lines to serum-free media. Five methods are presented that are designed for adapting hybridomas to a protein-free medium. These protocols may require some modifications for your particular cell line and conditions. - [Read Adapting Cells to a Serum-Free Environment Protocol]

Adherent Cell Types Infection Protocol - http://www.med.umich.edu/vcore/protocols/RetroviralCellScreenInfection101705.pdf

Category: Cloning Protocols: Vector Protocols

Protocol for infection for adherent cell types. - [Read Adherent Cell Types Infection Protocol]

Affinity Purification of Interacting Proteins from Cell Lysates Protocol - http://www.cshprotocols.org/cgi/content/abstract/2007/3/pdb.prot4593

Category: Chromatography Protocols: Affinity Chromatography Protocols

Recombinant protein or a chemically synthesized bioactive fragment is immobilized on resin and used as a probe to capture interacting proteins directly from a cell extract. Affinity-purified proteins are fractionated by gel electrophoresis and visualized by Coomassie staining. Proteins that interact specifically are identified by comparing this gel profile to one obtained from cell lysates passed over a control resin lacking the immobilized probe protein. - [Read Affinity Purification of Interacting Proteins from Cell Lysates Protocol]

Aggregation of ES cells and eight cell stage embryos - http://web.archive.org/web/20021020163836/grimwade.biochem.unimelb.edu.au/bowtell/cellbiol/sect65.htm#Aggregation%20of%20ES%20cells%20and%20eight%20cell%20stage%20embryos

Category: Cell Biology and Cell Culture: ES Stem Cell Biology and Culture

Aggregation of ES cells and eight cell stage embryos. Bowtell Lab. - [Read Aggregation of ES cells and eight cell stage embryos]

Aggregation of ES Cells with Mouse Morula- Stage Embryos Protocol - http://fds.oup.com/www.oup.co.uk/pdf/pas/13-10-6.pdf

Category: Stem Cell Protocols: Stem Cell Culture Protocols

Protocol for the aggregation of ES cells with mouse morula-stage embryos. Includes: Preparation of aggregation walls; ES cell preparation; Embryo preparation and aggregation. - [Read Aggregation of ES Cells with Mouse Morula- Stage Embryos Protocol]

Aggregation: Production of Chimerae - http://transgenics.ufscc.ufl.edu/TCF05agg_instruct.html

Category: Cell Biology and Cell Culture: ES Stem Cell Biology and Culture: ES Cell Aggregations - Production of Chimerae

Aggregation: Production of Chimerae. Detailed ES cell growth and preparation information for aggregations. Edward W. Scott Univ. Florida Shands Cancer Center - [Read Aggregation: Production of Chimerae]

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]

An Integrative Procedure For Apoptosis Identification And Measurement - http://www.natureprotocols.com/2006/08/03/an_integrative_procedure_for_a.php

Category: Cell Biology and Cell Culture: Apoptosis Protocols: Apoptosis Analysis

An Integrative Procedure for Apoptosis Identification and Measurement. Yingyu Cui Lab/Group: National Key Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences. I have uploaded an integrative procedure through which a relatively satisfactory result can be obtained following a single stage of cell culture and transient cell treatment, then detection with different instruments. This shortens experiment time. - [Read An Integrative Procedure For Apoptosis Identification And Measurement]

Analysis of Cellular DNA Content by Flow Cytometry Protocol - https://catalog.invitrogen.com/index.cfm?fuseaction=iProtocol.unitSectionTree&treeNodeID=9E661C8A9C23374B5FAB0610666CCDFB&objectid=6674F58BDEF6DCA5276258FEA4CD534D

Category: Cell Biology and Cell Culture: Flow Cytometry Protocols: DNA Staining Protocols for Flow Cytometry

Simple and universally applicable methods for staining fixed cells are presented, as are methods that utilize detergents and proteolytic treatment to permeabilize cells. Additionally, supravital cell staining with Hoechst 33342, which is primarily used for sorting live cells for subsequent culturing based on DNA-content differences, is also described. Also presented are methods for staining of cell nuclei isolated from paraffin-embedded tissues, and deconvolution of DNA-content-frequency... - [Read Analysis of Cellular DNA Content by Flow Cytometry Protocol]

Analysis of DNA Fragmentation Using Agarose Gel Electrophoresis (Subscription Required) - http://www.cshprotocols.org/cgi/content/extract/2006/1/pdb.prot4429

Category: Cell Biology and Cell Culture: Apoptosis Protocols: Apoptosis Analysis

Analysis of DNA Fragmentation Using Agarose Gel Electrophoresis Shailaja Kasibhatla et al. This protocol provides a qualitative method for assessing cell death by detecting DNA fragments using agarose gel electrophoresis. One of the classic features of apoptosis is the cleavage of the genomic DNA into oligonucleosomal fragments represented by multiples of 180-200 bp. Visualizing these fragments can aid in characterizing an apoptotic event. May be combined with more quantitative methods. - [Read Analysis of DNA Fragmentation Using Agarose Gel Electrophoresis (Subscription Required)]

Analysis of DNA Fragmentation Using Propidium Iodide (PI) Staining After Ethanol Fixation Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/1/pdb.prot4431

Category: Cell Biology and Cell Culture: Flow Cytometry Protocols: DNA Staining Protocols for Flow Cytometry

This protocol provides a method for analysis of DNA fragmentation using flow cytometry after propidium iodide (PI) labeling of fixed apoptotic cells. Flow cytometry reveals apoptotic nuclei in the subdiploid region of the cell cycle histogram... - [Read Analysis of DNA Fragmentation Using Propidium Iodide (PI) Staining After Ethanol Fixation Protocol]

Analysis Of DNA Fragmentation Using The JAM Assay (Subscription Required) - http://www.cshprotocols.org/cgi/content/extract/2006/1/pdb.prot4432

Category: Cell Biology and Cell Culture: Apoptosis Protocols: Apoptosis Analysis

Analysis of DNA Fragmentation Using the JAM Assay. By Shailaja Kasibhatla et al., The JAM assay is based on labeling nuclear DNA of cycling cells with [3H]thymidine and harvesting samples on glass fiber filters. Apoptosis will generate DNA fragments small enough to pass through the glass fiber filter, resulting in decreased radioactivity of the particular sample. Cell-mediated cytotoxicity or cell killing mediated by cytotoxic T lymphocytes (CTL) can also be measured by this technique. - [Read Analysis Of DNA Fragmentation Using The JAM Assay (Subscription Required)]

Analysis of ES Cell Clones by Mini-Southern - http://www.imgen.bcm.tmc.edu/molgen/labs/bradley/mini-sou.txt

Category: Cell Biology and Cell Culture: ES Stem Cell Biology and Culture

Analysis of ES Cell Clones by Mini-Southern. Bradley's Lab, Texas. - [Read Analysis of ES Cell Clones by Mini-Southern]

Anatomy of a Comparative Gene Expression Study - http://www.cs.wustl.edu/~jbuhler//research/array/

Category: Genetics and Genomics: Cancer Genetics Protocols

Anatomy of a comparative gene expression study. Includes: Choosing Cell Populations; mRNA Extraction and Reverse Transcription; Fluorescent Labeling of cDNA's; Hybridization to a DNA Microarray; Scanning the Hybridized Array; Interpreting the Scanned Image. - [Read Anatomy of a Comparative Gene Expression Study]

Anatomy of a Comparative Gene Expression Study - http://www.cs.wustl.edu/~jbuhler//research/array/

Category: Microarray Protocols: Microarray Analysis Protocols

Information on anatomy of a comparative gene expression study. Includes: Choosing cell populations; mRNA Extraction and Reverse Transcription; Fluorescent labeling of cDNA's; Hybridization of DNA microarray; Scanning the hybridized array; Interpreting the scanned image. - [Read Anatomy of a Comparative Gene Expression Study]

Annexin V Protocol - http://www.cyto.purdue.edu/flowcyt/research/cytotech/apopto/data/chap16.htm

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

Annexin V, belonging to a recently discovered family of proteins, the annexins, with anticoagulant properties has proven to be a useful tool in detecting apoptotic cells since it preferentially binds to negatively charged phospholipids like PS in the presence of Ca2+ and shows minimal binding to phosphatidylcholine and sphingomyeline. Changes in PS asymmetry, which is analyzed by measuring Annexin V binding to the cell membrane, were detected before morphological changes associated with... - [Read Annexin V Protocol]

Annexin V Protocol for Flow Cytometry - http://www.niehs.nih.gov/research/atniehs/core/fc/protocols/annexin.cfm

Category: Cell Biology and Cell Culture: Flow Cytometry Protocols

Different cell types vary in their phosphatidylserine (PS) content, along with the amount of PS exposure on the cell surface after cell death. This protocol is a guideline for getting started, however it may be necessary to adjust the concentration of the Annexin V-FITC. - [Read Annexin V Protocol for Flow Cytometry]

Articles (1-10 of 28)

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.

Microinjection Pipettes Protocol

Microinjection Pipettes Preparation Protocol.

Acid Washing Microinjection Pipettes Protocol

Acid Washing of Glass microinjection pipettes protocol.

Paraffin Embedding Protocol

Paraffin Embedding Protocol for molecular profiling. This Paraffin Embedding Protocol describes the processing of the tissues into sections following ethanol fixation. Molecular profiling (MP) is a technique that is used to visualize the global patterns of RNA expression or protein expression in various cell types and disease processes.

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