1Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, 2Department of Pathology and Laboratory Medicine, Indiana University Health
This protocol describes qPCR detection of cytomegalovirus in formalin-fixed, paraffin-embedded biopsy tissue, which is rapid, sensitive, specific, and useful for interpreting equivocal hematoxylin and eosin or immunohistochemical staining patterns.
Published July 9, 2014. Keywords: Genetics, qPCR, cytomegalovirus, CMV, biopsy, real-time PCR, gastrointestinal, formalin-fixed, paraffin-embedded tissue
JoVE Application Notes
1Cell Signaling Technology
Immunohistochemistry (IHC) is a technique used to analyze protein expression in the context of tissue morphology. This article describes an IHC protocol optimized by scientists at Cell Signaling Technology, for use with our antibodies, that you can replicate to obtain the best results in your experiments.
Published April 10, 2014. Keywords: Immunohistochemistry, IHC, paraffin, SignalStain, antibody, DAB, unmasking, antigen retrieval, Cell Signaling Technology, CST.
1Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry
Archival formalin fixed and paraffin embedded (FFPE) clinical samples are valuable material for investigation of diseases. Here we demonstrate a sample preparation workflow allowing in-depth proteomic analysis of microdissected FFPE tissue.
Published September 2, 2013. Keywords: Chemistry, Clinical Chemistry Tests, Proteomics, Proteomics, Proteomics, analytical chemistry, Formalin fixed and paraffin embedded (FFPE), sample preparation, proteomics, filter aided sample preparation (FASP), clinical proteomics; microdissection, SAX-fractionation
JoVE Clinical and Translational Medicine
1The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, 2Department of Oncology, The Johns Hopkins University School of Medicine, 3Department of Dermatology, The Johns Hopkins University School of Medicine, 4Department of Surgery, Johns Hopkins University School of Medicine, 5The Sol Goldman Pancreatic Cancer Center, The Johns Hopkins University School of Medicine, 6Yale Cancer Center, Yale School of Medicine, 7The Skip Viragh Center for Pancreatic Cancer, The Johns Hopkins University School of Medicine, 8Department of Pathology, The Johns Hopkins University School of Medicine
B7-H1 (PD-L1) and its binding to PD-1 provide a major tumor-induced immunosuppressive signal in the tumor’s microenvironment. An immunohistochemical staining technique to characterize the expression and localization of B7-H1 in pancreatic adenocarcinoma is described here.
Published January 3, 2013. Keywords: Cancer Biology, Medicine, Immunology, Biochemistry, Molecular Biology, Cellular Biology, Chemistry, Oncology, immunohistochemistry, B7-H1 (PD-L1), pancreatic adenocarcinoma, pancreatic cancer, pancreas, tumor, T-cell immunity, cancer
1Department of Cellular and Molecular Medicine, University of California, San Diego, 2Biosecurity and Public Health, Los Alamos National Laboratory
Unfixed frozen tissue samples embedded in Optimal Cutting Temperature medium (OCT) can be used to study natural distribution and glycosylation of secreted mucus. In this approach tissue processing is minimal and the natural presentation of glycolipids, mucins and glycan-epitopes is preserved. Tissue sections can be analyzed by immunohistochemistry using fluorescence or chromogenic detection.
Published September 21, 2012. Keywords: Medicine, Cellular Biology, Molecular Biology, Immunology, Biomedical Engineering, mucus, lectins, OCT, imaging, sialic acids, glycosylation
1Institute of Immunology & Experimental Oncology, Center for Biomedical Education and Research (ZBAF), Witten/Herdecke University
Cell migration is a biological phenomenon that is involved in a plethora of physiological, such as wound healing and immune responses, and pathophysiological processes, like cancer. The 3D-collagen matrix migration assay is a versatile tool to analyze the migratory properties of different cell types within in a 3D physiological-like environment.
Published October 5, 2014. Keywords: Bioengineering, cell migration, 3D collagen matrix, cell tracking
JoVE Clinical and Translational Medicine
1Department of Neurosurgery, Henry Ford Hospital
Protocol for propagation of dissociated high grade glioma surgical specimens in serum-free neurosphere medium to select for cells with cancer stem cell phenotype. For specimens that fail to grow as neurospheres, an alternative protocol is suggested. A paraffin embedding technique for maintaining the 3D neurosphere architecture for immunocytochemistry is described.
Published January 7, 2014. Keywords: Medicine, Primary Cell Culture, animal models, Nervous System Diseases, Neoplasms, glioblastoma, neurosphere, surgical specimens, long-term self-renewal
1Department of Integrative Oncology, BC Cancer Research Centre, 2Interdisciplinary Oncology Program, University of British Columbia - UBC, 3Photography/Video Production, Multi-Media Services, BC Cancer Agency, 4Department of Pathology and Laboratory Medicine, University of British Columbia - UBC
This video demonstrates the protocol for DNA extraction from formalin-fixed paraffin-embedded material. This is a multi-day procedure in which tissue sections are deparaffinized with xylene, rehydrated with ethanol and treated with proteinase K to purify and isolate DNA for subsequent gene-specific or genome-wide analysis.
Published March 26, 2011. Keywords: Genetics, DNA extraction, paraffin embedded tissue, phenol:chloroform extraction, genetic analysis, epigenetic analysis
1Department of Biological Sciences, Union College
By combining methods for RNA whole mount in situ hybridization and histology, gene expression can be linked with cell fate decisions in the developing embryo. These methods have been adapted to marine elasmobranchs and facilitate the use of these animals as model organisms for biomedical, toxicology and comparative studies.
Published April 12, 2013. Keywords: Genetics, Developmental Biology, Molecular Biology, Cellular Biology, Anatomy, Physiology, Biochemistry, Marine Biology, Disciplines and Occupations, whole mount in situ hybridization, RNA in situs, RNA, acid mucins, alcian blue, nuclear fast red stain, elasmobranch, marine elasmobranchs, L. erinacea, Shh, Hoxa13, gene expression, hybridization, histology, skate, embryos, animal model
1Cold Spring Harbor Laboratory
The in situ hybridization protocol described here allows a direct localization of mRNA and small RNA expression at the cellular level with high sensitivity and specificity. The procedure is optimized for paraffin-embedded plant tissue sections, is applicable to a wide range of plants and tissues, and can be completed within ten days.
Published November 23, 2011. Keywords: Plant Biology, In Situ hybridization, RNA localization, expression analysis, plant, DIG-labeled probe