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Clonality - X Chromosome Inactivation Assay Protocol - http://cgap-mf.nih.gov/Protocols/DNARNAProteomicAnalysis/DNA/DNAProtocols/Clonality.html

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]

Collection and Storage of Cotton Leaf Tissue - http://wheat.pw.usda.gov/~lazo/methods/lazo/collect.html

Category: Plant Biology Protocols

Protocol for the collection and storage of cotton leaf tissue. - [Read Collection and Storage of Cotton Leaf Tissue]

Confocal Microscopy Specimen Preparation Using Synthetic Fluorophores and Immunofluorescence - http://www.olympusconfocal.com/applications/protocols/index.html

Category: Microscopy Protocols: Confocal Microscopy Protocols

Includes staining protocols: Triple-Staining Adherent Cells with MitoTracker, Phalloidin,& Nuclear Dyes; Staining Adherent Cells with Cytokeratin Primary Antibodies & Synthetic Fluorophores; Staining Adherent Cells with Intermediate Filament Primary Antibodies & Synthetic Fluorophores; Staining Cells & Tissue Cryosections with Tubulin Primary Antibodies, Phallotoxins,& Synthetic Fluorophores; Triple-Staining Tissue Cryosections with Wheat Germ Agglutinin, Phalloidin,& Nuclear Dyes; etc. - [Read Confocal Microscopy Specimen Preparation Using Synthetic Fluorophores and Immunofluorescence]

Congo Red Putcher's Modification Amyloid Protocol - http://library.med.utah.edu/WebPath/HISTHTML/MANUALS/CONGORED.PDF

Category: Neuroscience Protocols: Neuronal Stains Protocols: Stains for Senile Plaques Protocols

Protocol to demonstrate amyloid deposits in tissue sections. When stained with the Congo Red Stain the amyloid, with the aide of polarizing lenses, will birefringe an apple green color. Under the microscope. - [Read Congo Red Putcher's Modification Amyloid Protocol]

Connective Tissue Stain for Muscle Biopsy Protocol - http://www.nottingham.ac.uk/pathology/protocols/gomori.html

Category: Neuroscience Protocols: Histology Stains Protocols: Connective Tissue Stains Protocols

Protocol for connective tissue stain for muscle biopsy. Gomori Trichome. - [Read Connective Tissue Stain for Muscle Biopsy Protocol]

Connective tissue Stain Protocol - http://www.nottingham.ac.uk/pathology/protocols/vangies.html

Category: Neuroscience Protocols: Histology Stains Protocols: Connective Tissue Stains Protocols

Protocol for connective tissue stain. - [Read Connective tissue Stain Protocol]

Counterstains Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/1/pdb.prot4338

Category: Cell Culture Protocols: Cell Staining Protocols

Counterstains are used to help differentiate the various cell types of subcellular structures seen in cell staining. They are essential for tissue sections, allowing the identification of the cell types, but also may be helpful in other staining reactions. - [Read Counterstains Protocol]

Cryosectioning Protocol - http://genetics.med.harvard.edu/~cepko/protocol/mike/C7.html

Category: Immunohistochemistry Protocols: Cryosectioning Protocols

Protocol for cryosectioning. While the timing of the various steps in this protocol are probably not critical, process the tissue all at once to ensure that RNA and/or proteins do not get degraded. Includes: 20% Paraformaldehyde/4% Paraformaldehyde-PBS; Sucrose/PBS. - [Read Cryosectioning Protocol]

De Novo Isolation of Embryonic Stem (ES) Cell Lines from Blastocysts Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/16/pdb.prot4403

Category: Stem Cell Protocols: Stem Cell Isolation Protocols

The starting material for de novo isolation of stem cell lines can be either normal 3.5-days post coitum (dpc) expanded blastocysts or "delayed" blastocysts. Delayed blastocysts are usually collected 4-6 days after ovariectomy. For both groups of blastocysts, tissue culture procedures are similar. The only difference is the timing of the first disaggregation, because delayed blastocysts will initially grow more slowly. - [Read De Novo Isolation of Embryonic Stem (ES) Cell Lines from Blastocysts Protocol]

Derivation of Mouse Embryonic Fibroblasts (MEF) Part I PDF - http://www.wicell.org/uploads/media/Protocols_Part_1_05.pdf

Category: Cell Biology and Cell Culture: ES Stem Cell Biology and Culture: MEF Protocols Mouse Embryonic Fibroblasts

WiCell Research Institute. Recipes, Frequently Asked Questions, Mouse Embryo Extraction and Tissue, Harvesting Mouse Embryonic Fibroblasts (MEF)from mice. - [Read Derivation of Mouse Embryonic Fibroblasts (MEF) Part I PDF]

Detect and Quantitate MicroRNA in Laser Capture Microdissection Samples - http://www.ambion.com/techlib/tn/131/6.html

Category: RNAi Technology Protocols

Information on how detect and quantitate MicroRNA in laser capture microdissection samples. Includes: Obtain Laser Capture Microdissected Samples; Isolate miRNA from LCM Samples; Quantitate miRNA by qRT-PCR; Detection of miRNA in Microdissected Tissue from Mouse Brain by qRT-PCR; Differential Expression of MicroRNA in Whole Brain Tissue Compared to a More Homogeneous Population of Cells. - [Read Detect and Quantitate MicroRNA in Laser Capture Microdissection Samples]

Detection of ß-Galactosidase and Alkaline Phosphastase Activities in Tissue Protocol - http://genetics.med.harvard.edu/~cepko/protocol/xgalplap-stain.htm

Category: Neuroscience Protocols: Histology Stains Protocols: Enzyme Histochemical Stains Protocols

Protocol for detection of ß-Galactosidase and alkaline phosphastase activities in tissue. - [Read Detection of ß-Galactosidase and Alkaline Phosphastase Activities in Tissue Protocol]

Detection of HPV 11 DNA in Paraffin-Embedded Laryngeal Tissue with a DIG-Labeled DNA Probe Protocol - http://www.roche-applied-science.com/PROD_INF/MANUALS/InSitu/pdf/ISH_143-148.pdf

Category: Cytogenetics Protocols: In Situ Hybridization Tissue Sections Protocols

Protocol for detection of HPV 11 DNA in paraffin-embedded laryngeal tissue with a DIG-labeled DNA probe. Includes: Probe preparation; Pretreatment of slides; Preparation of tissue sections; Hybridization; Washes; Detection of hybrids. - [Read Detection of HPV 11 DNA in Paraffin-Embedded Laryngeal Tissue with a DIG-Labeled DNA Probe Protocol]

Detection of mRNA in Tissue Sections Using DIG-labeled RNA and Oligonucleotide Probes Protocol - http://www.roche-applied-science.com/PROD_INF/MANUALS/InSitu/pdf/ISH_149-163.pdf

Category: Cytogenetics Protocols: In Situ Hybridization Tissue Sections Protocols

Protocol for detection of mRNA in tissue sections using DIG-labeled RNA and oligonucleotide probes. - [Read Detection of mRNA in Tissue Sections Using DIG-labeled RNA and Oligonucleotide Probes Protocol]

Detection of Protein Phosphorylation in Tissues and Cells Protocol - https://catalog.invitrogen.com/index.cfm?fuseaction=iProtocol.unitSectionTree&objectId=6677CD53C088A0E7A7B22F422FFCDC12&treeNodeId=9E6639B7FED0C828BBFE860A8E957694

Category: Immunology: Immunoprecipitation Protocols: Immunoprecipitation of Radiolabeled Cells Protocols

Most powerful and convincing method to determine if a specific protein is phosphorylated in a physiologically relevant manner is to assay phosphorylation in situ. The procedure described involves incubating cultured cells (e.g., primary neuronal cultures or transfected cells) or tissue preparations (e.g., hippocampal slices) with [32P]orthophosphate, which is then taken up by the cells or tissues and incorporated into the γ-phosphate position of ATP. - [Read Detection of Protein Phosphorylation in Tissues and Cells Protocol]

Determination of Neopterin and Biopterin by Liquid Chromatography Protocol - http://www.natureprotocols.com/2006/10/13/determination_of_neopterin_and.php

Category: Chromatography Protocols: Liquid Chromatography Protocols

Protocol for determination of neopterin and biopterin by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) in rat and human plasma, cell extracts and tissue homogenates. - [Read Determination of Neopterin and Biopterin by Liquid Chromatography Protocol]

Determination of Tissue Fungal Burden Utilizing Quantitative Real Time Polymerase Chain Reaction - http://www.sacmm.org/pdf/Determination%20of%20Tissue%20Fungal%20Burden%20utilizing%20Quantitative%20Real%20Time%20PCR.pdf

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]

Differential Display-PCR Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/2/pdb.prot3844

Category: PCR Protocols

Method uses PCR to amplify and display many cDNAs derived from the mRNAs of a given cell or tissue type. The method relies on two different types of synthetic oligonucleotides: anchored antisense primers and arbitrary sense primers. A typical anchored primer is complementary to approx. 13 nucleotides of the poly(A) tail of mRNA and the adjacent two nucleotides of the transcribed sequence. - [Read Differential Display-PCR Protocol]

Dissociation of Mouse Spleen and Hemopoietic Tissue Protocol - http://icg.cpmc.columbia.edu/cattoretti/Protocol/mousepathology/DissociationSpleen.html

Category: Mouse Protocols

Protocol for the dissociation of mouse spleen and hemopoietic tissue. - [Read Dissociation of Mouse Spleen and Hemopoietic Tissue Protocol]

DNA Extraction Technique for Biopsy Tissue Protocol - http://genome-lab.ucdavis.edu/Protocols/DNA%20extraction%20technique%20for%20biopsy%20tissue.htm

Category: Genetics and Genomics: Cancer Genetics Protocols

Protocol for DNA extraction technique for biopsy tissue. - [Read DNA Extraction Technique for Biopsy Tissue Protocol]

DNA Extraction Technique for Biopsy Tissue Protocol - http://genome-lab.ucdavis.edu/Protocols/DNA%20extraction%20technique%20for%20biopsy%20tissue.htm

Category: Nucleic Acid Purification Protocols: DNA Isolation Protocols

Protocol for DNA extraction technique for biopsy tissue. - [Read DNA Extraction Technique for Biopsy Tissue Protocol]

DNA preparation by cryotom tissue dissection - http://amba.charite.de/cgh/protocol/02/mapeng02.htm

Category: Cytogenetics Protocols: Comparative Genomic Hybridization CGH Protocols

DNA preparation by cryotom tissue dissection for CGH Comparative Genomic Hybridization. Institute of Pathology "Rudolf- Virchow-Haus" University Hospital CharitÃ© - [Read DNA preparation by cryotom tissue dissection]

Dnase-chip Protocol - http://www.natureprotocols.com/2006/07/03/dnasechip_a_high_resolution_me.php

Category: Microarray Protocols: Microarray Chip Protocols

Dnase-chip: A High Resolution Method to Identify DnaseI Hypersensitive Sites using Tiled Microarrays. This method can be applied globally or in a targeted fashion to any tissue from any species with a sequenced genome. - [Read Dnase-chip Protocol]

Double Immunofluorescence Staining for BCL-6 Protocol - http://icg.cpmc.columbia.edu/cattoretti/Protocol/immunohistochemistry/DoubleIFstain.html

Category: Immunology: Immunofluorescence Protocols: Immunofluorescence Staining Protocols

Protocol for double immunofluorescence staining for BCL-6. Any type of tissue is suitable for this technique, as long as the antigenicity for your antigen(s) is preserved. Includes: unfixed or acetone-fixed specimens; dewaxed, antigen retrieved slides. - [Read Double Immunofluorescence Staining for BCL-6 Protocol]

Elastic and Connective Tissue Stain Protocol - http://www.nottingham.ac.uk/pathology/protocols/evg.html

Category: Neuroscience Protocols: Histology Stains Protocols: Connective Tissue Stains Protocols

Protocol for elastic and connective tissue stain. Elastic Van Gieson (EVG). - [Read Elastic and Connective Tissue Stain Protocol]

Articles (1-10 of 11)

Populational Analysis of Genomic DNA Protocol

A protocol on the populational Analysis of genomic DNA.

Drosophila Cell Transfection Protocol

A simple Drosophila tissue culture cell transfection method.

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.

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.