mammalian Protocols

Category: Microscopy Protocols: Live-Cell Imaging Protocols

This protocol describes a method for observing and measuring the movement of RNA molecules in the nucleus of living mammalian cells. Caged fluorescein-labeled DNA oligonucleotides are introduced into living mammalian cells, where they demonstrably hybridize to complementary RNA. After site-specific photoactivation at desired sites within the cell, the RNA movements away from those sites are followed and digitally recorded using a rapid acquisition microscopy system. - [Read Photoactivation-Based Labeling and In Vivo Tracking of RNA Molecules in the Nucleus]

Category: Cell Organelle Protocols: Subcellular Fractionation Protocols

The employment of differential centrifugation to prepare crude fractions of subcellular particles from homogenates is often a necessary first step to a subsequent purification of one or more particles on a density gradient. This protocol describes the use of differential centrifugation to fractionate a mammalian liver homogenate but similar methods should be applicable to all mammalian tissues and cultured cells. - [Read Preparation of Crude Subcellular Fractions by Differential Centrifugation Protocol]

Category: Nucleic Acid Electrophoresis Protocols: Pulsed Field Gel Electrophoresis Protocols

Protocol for preparation of DNA for pulsed-field gel electrophoresis: isolation of DNA from mammalian cells and tissues. Genomic DNAs from mammalian cells are prepared for pulsed-field gel electrophoresis by lysing cells in situ in an agarose plug.  Following digestion with an appropriate restriction enzyme, the plug is loaded directly into the well of a pulsed-field gel or it can be melted before loading. - [Read Preparation of DNA for Pulsed-field Gel Electrophoresis: Isolation of DNA from Mammalian Cells]

Category: Proteomic Protocols

Preparation of whole cell homogenates of cultured mammalian cells for 2-D Electrophoresis. Univ. Virginia. - [Read Preparation of whole cell homogenates of cultured mammalian cells for 2-D Electrophoresis]

Category: Cell Biology and Cell Culture: Cell Transfection Protocol

Lipofectamine transient tranfection of mammalian cells in IMDM cell media. Julie B. Wolf, UMBC. - [Read Procedure for Transfection of Mammalian Cells Using Lipofectamine]

Category: Cell Biology and Cell Culture: Endothelial Cell Protocols

Primary mammalian endothelial cells protocol. This protocol is designed for primary endothelial cells isolated from various organs of mammals. Large and flat cells, often with large nuclei. Includes: Required reagents; DNA preparation and quality; Preparation of cells and cell culture; Important controls; Nucleofection protocol. - [Read Protocol Primary Mammalian Endothelial Cells]

Category: Cell Organelle Protocols: Subcellular Fractionation Protocols: Membrane Isolation Protocols

This protocol uses a "light mitochondrial" pellet from a mammalian liver homogenate. The gradient thus has to resolve a variety of denser components (peroxisomes, lysosomes, mitochondria) from the Golgi membranes, which have a low density in iodixanol (1.06-1.09 g/ml) [1]. The protocol is specifically tailored to the purification of Golgi membranes from this pellet and is unsuitable for the isolation or analysis of other organelles present in the light mitochondrial fraction. - [Read Purification of Golgi Membranes from a Light Mitochondrial Fraction in a Self-Generated Gradient]

Category: Cell Organelle Protocols: Subcellular Fractionation Protocols: Mitochondria Isolation Protocols

This protocol describes a discontinuous gradient, which resolves the mitochondria from both lighter and denser organelles. Because the centrifugation is carried out for 4 h, diffusion will create a partially continuous gradient and this probably contributes to the resolution of the mitochondria from the lighter lysosomes. - [Read Purification of Mammalian Liver Mitochondria by Flotation Through a Pre-formed Discontinuous Iodixan]

Category: Cell Organelle Protocols: Subcellular Fractionation Protocols: Peroxisome Isolation Protocols

Peroxisomes can be purified in self-generated iodixanol gradients in high yield (80-90%) with no detectable contamination from any other organelle. In iodixanol peroxisomes are the densest of the major subcellular organelles (ρ = 1.18-1.20 g/ml) present in the light mitochondrial fraction from mammalian tissues and cells. - [Read Purification of Peroxisomes in a Self-Generated Gradient]

Category: Nucleic Acid Purification Protocols: DNA Isolation Protocols: DNA Isolation from Mammalian Cells Protocols

Mammalian DNA prepared from blood or tissues as described in this protocol is 20-50 kb in size and suitable for use as a template in PCRs.  The yields of DNA vary between 0.5 and 3.0 µg/mg tissue or 5 and 15 µg per 300 µl of whole blood. - [Read Rapid Isolation of Mammalian DNA Protocol]

Category: Nucleic Acid Electrophoresis Protocols: Pulsed Field Gel Electrophoresis Protocols

Protocol for restriction endonuclease digestion of DNA in agarose plugs. Genomic DNA isolated from mammalian, yeast, or bacterial cells can be digested with restriction endonucleases by incubating agarose plugs containing the DNA in the presence of the desired enzyme.  After digestion, the DNA can be fractionated by pulsed-field gel electrophoresis and either isolated from the gel or analyzed by Southern Hybridization. - [Read Restriction Endonuclease Digestion of DNA in Agarose Plugs Protocol]

Category: DNA Protocols: cDNA Library Protocols: cDNA Library Construction Protocols

Two methods of screening pools of cloned cDNAs are discussed: transfection into mammalian cells and injection into Xenopus oocytes. - [Read Screening cDNA Libraries Constructed in Eukaryotic Expression Vectors Protocol]

Category: Chromatography Protocols: DNA RNA Affinity Chromatography

When many RNA samples are to be processed or when working with small amounts (<50 µg) of total mammalian RNA, the technique of choice is batch chromatography on oligo(dT)-cellulose. The method described in this protocol uses a combination of temperature and ionic strength to maximize binding and recovery of polyadenylated RNA. IMPORTANT: Prepare all reagents used in this protocol with Diethyl pyrocarbonate (DEPC)-treated H2O. Joseph Sambrook and David W. Russell. - [Read Selection of Poly(A)+ RNA by Batch Chromatography - Subscription Required]

Category: Chromatography Protocols: DNA RNA Affinity Chromatography

Chromatography on oligo(dT) columns is the preferred method for large-scale purification (>25 µg) of poly(A)+ RNA extracted from mammalian cells. Typically, between 1% and 10% of the RNA applied to the oligo(dT) column is recovered as poly(A)+ RNA. Because the method can be frustratingly slow, it is not recommended for purification of poly(A)+ RNA from multiple samples. For this purpose, batch elution (Selection of Poly(A)+ RNA by Batch Chromatography) is the better choice. - [Read Selection of Poly(A)+ RNA by Oligo(dT)-Cellulose Chromatography - Subscription Required]

Category: RNAi Technology Protocols: RNAi Mammalian Cells Protocols

To target a specific mRNA for degradation, a portion of the mRNA target sequence must be known, and a segment of the target mRNA must be chosen that will be used for targeting by the cognate siRNA duplex. Protocol describes the selection of siRNA sequences for mammalian RNAi. - [Read Selection of siRNA Sequences for Mammalian RNAi Protocol]

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

This protocol describes a method for testing of new serum lots prior to use in cell culture. Serum lots vary considerably in their ability to support cell growth, and some lots even contain toxic or growth-inhibitory compounds. It is advantageous to test serum lots and purchase in large volume, both for cost benefit. - [Read Serum Testing for Mammalian Cell Culture Protocol]

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

Protocol describes methods for maintaining healthy, dividing mammalian cells in culture and during imaging, when mitosis can be examined. Rose chambers are preferable for observation and microinjection of living mitotic cells, but slide/coverslip preparations are easy to make and do not require any special equipment. - [Read Studying Mitosis in Cultured Mammalian Cells Protocol]

Category: Cytogenetics Protocols

Protocol describes methods for maintaining healthy, dividing mammalian cells in culture and during imaging, when mitosis can be examined. Rose chambers are preferable for observation and microinjection of living mitotic cells, but slide/coverslip preparations are easy to make and do not require any special equipment. Another inexpensive and easy-to-use alternative is to grow cells in a culture dish with a glass bottom. Such dishes are suitable for microinjection experiments. - [Read Studying Mitosis in Cultured Mammalian Cells Protocol]

Category: Cell Biology and Cell Culture: Cell Cycle Protocols: Mitosis Protocols

Protocol describes methods for maintaining healthy, dividing mammalian cells in culture and during imaging, when mitosis can be examined. Rose chambers are preferable for observation and microinjection of living mitotic cells, but slide/coverslip preparations are easy to make and do not require any special equipment. Another inexpensive and easy-to-use alternative is to grow cells in a culture dish with a glass bottom. Such dishes are suitable for microinjection experiments. - [Read Studying Mitosis in Cultured Mammalian Cells Prtocol]

Category: Cell Biology and Cell Culture: Cell Cycle Protocols: Mitosis Protocols

Protocol describes a method for synchronizing monolayer cells in mitosis using selective detachment from their substrate. During mitosis, cells become spherical, causing them to become more loosely attached to their substrate. The "rounded up" cells are selectively detached by tapping the culture flask, resulting in a population in which as many as 90-98% of the cells are in mitosis. The drug nocodazole is used to increase the percentage of cells undergoing mitosis before detachment is performed - [Read Synchronization of Mammalian Cell Cultures in Mitosis Using Selective Detachment Protocol]

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

This protocol describes a method for synchronizing monolayer cells in mitosis using selective detachment from their substrate. During mitosis, cells become more spherical, causing them to become more loosely attached to their substrate. The "rounded up" cells are selectively detached by tapping the culture flask, resulting in a population in which as many as 90-98% of the cells are in mitosis. The drug nocodazole is used to increase the percentage of cells undergoing mitosis before detachment.. - [Read Synchronization of Mammalian Cell Cultures in Mitosis Using Selective Detachment Protocol]

Category: Transfection Protocols

DEAE-dextran is generally used to obtain a burst of transient expression of cloned genes after transfection of mammalian cells. Many variants of the technique have been described, all of which seek to maximize the uptake of DNA and to minimize the cytotoxic effects of DEAE-dextran. In this protocol cells are exposed briefly to a high concentration of DEAE-dextran-DNA and then to chloroquine diphosphate, which is a facilitator of transfection. - [Read Transfection Mediated by DEAE-Dextran: High-efficiency Method Protocol]

Category: Transfection Protocols

Protocol describes a method for the delivery of siRNAs into mammalian cells in the absence of reporter plasmids. This is best achieved with transfection reagents developed for the delivery of antisense oligodeoxynucleotides. The quantities of reagents given below are calculated for the transfection of one well of a 24-well plate. - [Read Transfection of Mammalian Cells with siRNA Duplexes Protocol]

Category: RNAi Technology Protocols: RNAi Mammalian Cells Protocols

Protocol describes a method for the delivery of siRNAs into mammalian cells in the absence of reporter plasmids.  This is best achieved with transfection reagents developed for the delivery of antisense oligodeoxynucleotides.  The quantities of reagents given below are calculated for the transfection of one well of a 24-well plate. - [Read Transfection of Mammalian Cells with siRNA Duplexes Protocol]

Category: Transfection Protocols: Transient Transfection Protocols

Transient transfection into mammalian cells is a convenient way to over express and obtain protein expression. Protocol includes: Culture conditions; Transfection of experimental cells; Preparation of Mammalian Cell Lysate for Luciferase assay. - [Read Transient Transfection and Luciferase assay]