populations Protocols

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]

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]

Category: Drosophila Protocols: Drosophila Culture Media Protocols

Protocol for the basic methods of culturing Drosophila. Includes: Stockkeeping; Culture contaminants; Experimental populations. - [Read Basic Methods of Culturing Drosophila Protocol]

Category: Cell Biology and Cell Culture: Cell Cycle Protocols

protocol describes a method for the synchronization of cell populations using centrifugal elutriation. The method relies on the fact that cell size increases linearly as cells proceed through the cell cycle. Cells of similar size (and cell cycle phase) are eluted stepwise from the cell chamber, with the smallest size (those in early G1) being eluted first. Using this procedure, it is possible to obtain relatively pure populations of cells at various points in G1, S, and G2/M. - [Read Cell Synchronization Using Centrifugal Elutriation Protocol]

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

This protocol describes a method for the synchronization of cell populations using centrifugal elutriation. The method relies on the fact that cell size increases linearly as cells proceed through the cell cycle. Cells of similar size (and cell cycle phase) are eluted stepwise from the cell chamber, with the smallest size (those in early G1) being eluted first. Using this procedure, it is possible to obtain relatively pure populations of cells at various points in G1, S, and G2/M. - [Read Cell Synchronization Using Centrifugal Elutriation Protocol]

Category: Cell Biology and Cell Culture: Flow Cytometry Protocols

Protocol uses specific antibodies coupled to one of four fluorochromes: fluorescein isothiocyanate (FITC), R-phycoerythrin (PE), peridinin chlorophyll-a (PcP), and allophycocyanin (APC). These fluorochromes can be used simultaneously to stain and analyze the expression patterns of four different proteins in the same sample. The fluorochrome stained cell populations are analyzed using a FACSCalibur dual-laser flow cytometer. - [Read Characterization of Cells by Flow Cytometry Protocol]

Category: Immunology: B Cell Protocols

Fluorochromes can be used simultaneously to stain and analyze the expression patterns of four different proteins in the same sample. The fluorochrome stained cell populations are analyzed using a FACSCalibur dual-laser flow cytometer. - [Read Characterization of Cells by Flow Cytometry Protocol]

Category: Genetics and Genomics: Cancer Genetics Protocols

Investigators can utilize X chromosome inactivation (methylation) to determine the clonality status of a tumor or premalignant lesion in females. The technique is based on a methylation-sensitive restriction enzyme and analysis of a polymorphic locus on the X chromosome. Clonal cell populations will show "loss" of the non-methylated allele after restriction digest. The assay can be performed on DNA recovered from microdissected samples. Both frozen tissue and fixed-embedded tissue can be used. - [Read Clonality - X Chromosome Inactivation Assay Protocol]

Category: Fungi Protocols: Neurospora Protocols

Information and tips on how to sample natural populations. - [Read How to Sample Natural Populations]

Category: Signalling Signal Transduction Protocols: Cytokine Protocols

Fluorescent anti-cytokine and monoclonal antibodies are useful for the intracellular staining and multiparameter flow cytometric analysis of individual cytokine-producing cells within mixed cell populations. BD Biosciences. - [Read Immunofluorescent Staining of Intracellular Cytokines for Flow Cytometric Analysis]

Category: Tetrahymena Protozoa Protocols

Protocol describes how to allow the isolation of nuclei from all stages of the Tetrahymena life cycle in high yield with a high degree of purity. This method gives highly purified populations of both micronuclei and macronuclei. - [Read Isolation and Purification of Tetrahymena Nuclei Protocol]

Category: Immunology: Mononuclear Cell Isolation Protocols: B Lymphocyte Isolation Protocols

A flow cytometry technique is presented, which results in the selection and isolation of two populations of cells from a complex mixture based on physical properties (e.g., size and internal granularity) and correlated expression of several surface molecules - [Read Isolation of Ly-1+/CD5+ B Cells by Cell Sorting Protocol]

Category: Immunology: T Cell Protocols

Peyer’s Patch, and Lamina Propria Cells lymphocyte populations should be analyzed when studying the immunological status of the intestine, for example in oral immunization or in intestinal disease (including infectious disease and tumors). This protocol details techniques for isolation of IEL, PP cells, and LP cells from the small intestine of the mouse. - [Read Isolation of Mouse Small Intestinal Intraepithelial Lymphocytes Protocol]

Category: Histology Protocols: Laser Capture and Microdissection

Laser Capture Microdissection of Living in vitro Cells. This PDF describes a precise, rapid and convenient Laser Capture Microdissection (LCM) method for the positive selection of living adherent cells and the successful subsequent re-cultivation of homogenous sub-populations. Arcturus. - [Read Laser Capture Microdissection of Living in vitro Cells PDF]

Category: Primary Cell Isolation and Culture Protocols: Laser Capture Microdissection Protocols

LCM technology can harvest the cells of interest directly or can isolate specific cells by cutting away unwanted cells to give histologically pure enriched cell populations. A variety of downstream applications exist: DNA genotyping and loss-of-heterozygosity (LOH) analysis, etc. Protocol provides a thorough description of LCM techniques, with an emphasis on tips and troubleshooting advice derived from LCM users. The total time required to carry out this protocol is typically 1–1.5 h. - [Read Laser-capture Microdissection Protocol]

Category: Yeast Cell Culture Protocols: Yeast Sporulation Protocols

Microneedles attached to micromanipulators are used in the dissection of tetrads, isolation of zygotes from populations of mating haploid cells, and manipulation of individual cells. - [Read Making a Tetrad Dissection Needle Protocol]

Category: Immunology

A method for ameliorating autoimmune disease by passive transfer of IVIg-primed leukocytes. Developed a method for ‘priming’ specific leukocyte populations with IVIg to study their potential role in ameliorating ITP upon passive transfer, which we describe herein. Using this technique, found that splenic CD11c+ dendritic cells reacted with IVIg, or several IVIg mimetic regimes, were primed to ameliorate ITP upon transfer to thrombocytopenic mice. - [Read Method for Ameliorating Autoimmune Disease by Passive Transfer of IVIg-Primed Leukocytes]

Category: Primary Cell Isolation and Culture Protocols: Laser Capture Microdissection Protocols

Human tissues are comprised of multiple interacting cell populations in a complex three dimensional arrangement with each cellular phenotype determined by a unique profile of mRNA and protein expression. Before microdissection techniques were developed, the only analysis tools for phenotypic studies were primarily immunohistochemistry and in-situ hybridization. While useful, these tools are limited to single gene analysis and, in general, do not allow qualitative studies. - [Read Microdissection Overview]

Category: Cell Biology and Cell Culture: Endothelial Cell Protocols

Endothelial cells, which line blood vessels, can be prepared from a variety of tissues. They are frequently prepared from the umbilical vein, which is relatively easy to obtain. The procedure is clearly described and provides a large population of highly purified endothelial cells. There are also methods for obtaining endothelial cells from other tissues such as fat, skin, and mucosa. These methods require special care and generate smaller populations of cells. - [Read Preparation of Endothelial Cells Protocol]

Category: Cell Biology and Cell Culture: Cell Cycle Protocols

This method works well to assess cell cycle distribution of whole cell populations. This method can also be used to assess the cell cycle distribution of GFP transfected cells however, the EtOH step is generally not sufficient to keep GFP in the cell. - [Read Preparing Cells for PI/FACS (cell cycle) Analysis Protocol]

Category: Immunology: B Cell Protocols

Describes procedures for measuring the capacity of purified B cells to undergo proliferation. The method centers on the use of polyclonal stimulating agents (mitogens) because these agents stimulate the majority of B cells and because the alternative (measurement of antigen-induced proliferation) requires the laborious procedures of isolating antigen-specific B cells (which are otherwise present in too low a concentration in whole B cell populations). - [Read Proliferative Assays for B Cell Function Protocol]

Category: Primary Cell Isolation and Culture Protocols

This method enables the isolation of different populations of liver cells and describes their subsequent culture. - [Read The Isolation and Culture of Rat Hepatic Cells Protocol]

Category: Pharmacology and Toxicology Protocols: Cytotoxicity Protocols: Liver Toxicity Assays Protocols

This method enables the isolation of different populations of liver cells and describes their subsequent culture. - [Read The Isolation and Culture of Rat Hepatic Cells Protocol]

Category: Plant Biology Protocols

Alfalfa is an outcrossing species, cultivars consist of populations rather than individual homozygous or inbred lines. After only two cycles of self-pollination, severe inbreeding depression eliminates selfed individuals from populations. To obtain sufficient plant material of relative genetically uniformity (these plants will still necessarily be heterozygous) for experimental purposes, it may be necessary to propagate a single individual or clone. - [Read Vegetative Propagation of Alfalfa by Stem Cuttings]