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2-D Polyacrylamide Gel Electrophoresis Protocol - http://cgap-mf.nih.gov/Protocols/DNARNAProteomicAnalysis/Proteomics/2DPage.html

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

Protocol for 2-D polyacrylamide gel electrophoresis. Includes: 50 ml IEF Lysis Buffer; 10X Electrophoresis Running Buffer (10 L); 30% Acrylamide Stock (1 liter); Separating Acrylamide Gel; 50 ml Equilibration Buffer I; 50 ml Equilibration Buffer II; Transfer Buffer; Sample Preparation; Tissue Processing; Reswelling; Prepare Gradient Acrylamide Gel (9-18%); Transfer and Sequencing of Proteins. - [Read 2-D Polyacrylamide Gel Electrophoresis Protocol]

Autoradiography and Reading of Sequencing Gels Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/2/pdb.prot3588

Category: DNA Protocols: DNA Sequencing Protocols

Protocol describes fixation of a sequencing gel and processingin preparation for autoradiography. - [Read Autoradiography and Reading of Sequencing Gels Protocol]

Color Changing Karyotyping (CCK) Protocol: An M-FISH/SKY Alternative - http://info.med.yale.edu/genetics/ward/tavi/CCKmethod.html

Category: Cytogenetics Protocols

Protocol for color changing karytoping (CCK): an M-FISH/SKY alternative. Includes: Slide preparation and hybridization; Probes, dyes and antibodies; Probe detection and image capture; Image processing. - [Read Color Changing Karyotyping (CCK) Protocol: An M-FISH/SKY Alternative]

Combined DNA In Situ Hybridization and Immunocytochemistry Protocol - http://www.roche-applied-science.com/PROD_INF/MANUALS/InSitu/pdf/ISH_127-134.pdf

Category: Cytogenetics Protocols: In Situ Hybridization Protocols

Protocol for combined DNA in situ hybridization and immunocytochemistry for the simultaneous detection of nucleic acid sequences, proteins, and incorporated BrdU in cell preparations. Includes: Cell preparations and BrdU labeling; Detection of antigen by immunocytochemistry (ICC); Visualization of ICC antigen; -Gal-BCIG reaction (for producing a blue precipitate visible under brightfield microscopy); Cell processing for in situ hybridization; In situ hybridization (ISH); etc... - [Read Combined DNA In Situ Hybridization and Immunocytochemistry Protocol]

Confocal Microscopy: Speciman Preparation and Imaging - http://www.microscopyu.com/articles/confocal/confocalintropreparation.html

Category: Microscopy Protocols: Confocal Microscopy Protocols

Basic information on confocal microscopy, includes: Specimen Preparation and Imaging; Objective Lens Parameters and Optical Section Thickness; The Objective Lens; Probes for Confocal Imaging; Autofluorescence; Collecting Images; Troubleshooting; Image Processing and Publication; - [Read Confocal Microscopy: Speciman Preparation and Imaging]

Dynamic Flow Assay for Cell Adhesion in a Parallel Plate Flow Chamber - http://www.glycotech.com/protocols/proto7.html

Category: Cell Biology and Cell Culture

Flow assays offer visualization of cell adhesion under wall shear stress. Visualization of the different events of cell adhesion can be quantified by selective image acquisition and subsequent image processing. Flow assays are suited for adhesive events which occur very rapidly in a time scale shorter than that of most static adhesion assays. Also, events subsequent to the initial events can be studied such as cell stabilization and spreading giving some insight into the kinetics of cell-cell. - [Read Dynamic Flow Assay for Cell Adhesion in a Parallel Plate Flow Chamber]

Dynamic Flow Assay in a Parallel Plate Flow Chamber - http://www.glycotech.com/protocols/proto7.html

Category: Cell Biology and Cell Culture: Cell Adhesion Protocols

Flow assays allow visualization of cell adhesion under well-defined wall shear stress. Visualization of the events of cell adhesion are quantified by selective image acquisition and image processing. Events subsequent to the initial events can be studied such as cell stabilization and spreading. John T. Patton~GlycoTech Corporation, Rockville, Maryland - [Read Dynamic Flow Assay in a Parallel Plate Flow Chamber]

Electron Microscope Lab protocols - http://biology.berkeley.edu/EML/protocols.html

Category: Molecular Imaging: Electron Microscopy Protocols

Generic processing protocol ï¿½ PLT/ LR Gold ï¿½ SEM Generic Processing protocol ï¿½ SEM Microwave tissue processing protocol ï¿½ Uranyl acetate and Lead citrate ...Electron Microscope Lab protocols at UC Berkeley - [Read Electron Microscope Lab protocols]

ELECTRON MICROSCOPY (EM) protocols and methods - http://www.bristol.ac.uk/vetpath/cpl/emtechs.htm

Category: Molecular Imaging: Electron Microscopy Protocols

E.M. processing schedule - epoxy resin E.M. processing schedule - acrylic resin Primary fixative and buffers Veterinary Pathology. ELECTRON MICROSCOPY (EM) protocols and methods - [Read ELECTRON MICROSCOPY (EM) protocols and methods]

FASC Analysis of Cell Cycle using BrdU and PI Protocol - http://www.niehs.nih.gov/research/atniehs/core/fc/protocols/fasc.cfm

Category: Cell Biology and Cell Culture: Flow Cytometry Protocols

Protocols for FASC analysis of cell cycle using BrdU and PI. Includes: Labeling of Cells with BrdU; Collecting the Cells; Processing the Cells. - [Read FASC Analysis of Cell Cycle using BrdU and PI Protocol]

Fixation and Fixatives - A great guide - http://home.primus.com.au/royellis/fix.htm

Category: Histology Protocols: Fixation of Cells Tissues Protocol

Fixation is to preserve cells and tissue constituents in as close a life-like state as possible and to allow them to undergo further preparative procedures without change. Fixation arrests autolysis and bacterial decomposition and stabilises the cellular and tissue constituents so that they withstand the subsequent stages of tissue processing. Great detailed guide with protocols. Anthony S-Y Leong. - [Read Fixation and Fixatives - A great guide]

Frozen Sectioning and Tissue Sectioning for Electron Microscopy - http://www.ucsf.edu/pathol/research/morphprotocol.htm

Category: Histology Protocols: Tissue Sample Sectioning

Frozen Sectioning and Tissue Sectioning for Electron Microscopy. Includes Tissue Processing for Transmission Electron Microscopy and Tissue Preservation for Light Microscopy. University of California UCSF Dept. Pathology Research. - [Read Frozen Sectioning and Tissue Sectioning for Electron Microscopy]

Histotechniques - Manual - http://medlib.med.utah.edu/WebPath/HISTHTML/HISTOTCH/HISTOTCH.html

Category: Histology Protocols

Histotechniques - Manual. Great Histology Protocol Handbook. Includes: Tissue Processing, Specimen Accessioning, Fixation, Fixatives, Tissue Processing, Sectioning, H and E staining, more. - [Read Histotechniques - Manual]

Histotechniques Fixation - http://library.med.utah.edu/WebPath/HISTHTML/HISTOTCH/HISTOTCH.html

Category: Immunohistochemistry Protocols: Fixation Protocols

Information on histotechniques. Includes: Fixation - types of fixatives; factors affecting fixation; General usage of fixatives; Tissue Processing; Sectioning; Frozen Sections; Staining; H and E staining; Coverslipping; Decalcification; Artefacts in Histologic Sections; Problems in Tissue Processing. - [Read Histotechniques Fixation]

Image Processing Tools - http://depts.washington.edu/keck/leica/ip.html

Category: Molecular Imaging

Image Processing Tools. Keck Imaging Center - [Read Image Processing Tools]

ImageJ - Image Processing and Analysis in Java - http://rsb.info.nih.gov/ij/

Category: Molecular Imaging

ImageJ - Image Processing and Analysis in Java. Useful program for MacOs MacosX and PC. Analysis includes: Measure area, mean, standard deviation, min and max of selection or entire image. Measure lengths and angles. Use real world measurement units s - [Read ImageJ - Image Processing and Analysis in Java]

In vitro Translation Assays for CFTR - http://pen2.igc.gulbenkian.pt/cftr/vr/c/ostedgaard_in_vitro_translation_assays_for_cftr.pdf

Category: Cell Biology and Cell Culture: In Vitro Reconstitution Protocols

Protocol outlines the general procedure and requirements for in vitro translation of CFTR and outlines some assays using in vitro translated product. Core glycosylation of CFTR occurs in the ER. An assay for this processing step requires the addition of microsomal membranes to the basic in vitro translation mixture. This protocol takes this into account. - [Read In vitro Translation Assays for CFTR]

Live Cell Spinning Disk Confocal Fluore Imaging of Cells- Colocalization of Fluorescent Protein Tags - http://www.signaling-gateway.org/data/cgi-bin/ProtocolFile.cgi/afcs_PP00000143.pdf?pid=PP00000143

Category: Microscopy Protocols: Confocal Microscopy Protocols

Protocol describes the acquisition and processing of confocal fluorescent and bright field images of live cells, expressing cyan fluorescent protein(CFP) and/or yellow fluorescent protein (YFP), with a spinning disk confocal head on a Zeiss Axiovert 200 M microscope. This procedure is used to help determine if N- or Cterminal tagging of signaling molecules alters the steady state localization pattern of the signaling protein in question. - [Read Live Cell Spinning Disk Confocal Fluore Imaging of Cells- Colocalization of Fluorescent Protein Tags]

Live Cell Spinning Disk Confocal Fluorescence Imaging of Cells- YFP & Bright Field—Three Z Axis - http://www.signaling-gateway.org/data/cgi-bin/ProtocolFile.cgi/afcs_PP00000144.pdf?pid=PP00000144

Category: Microscopy Protocols: Confocal Microscopy Protocols

Protocol describes the acquisition and processing of confocal fluorescent and bright field images of live cells expressing yellow fluorescent protein (YFP), with a spinning disk confocal head on a Zeiss Axiovert 200 M microscope when three planes along the z-axis of the cell are acquired. Protocol includes: Description of Microscope and Imaging Setup; Description of Acquisition Parameters; Image Processing. - [Read Live Cell Spinning Disk Confocal Fluorescence Imaging of Cells- YFP & Bright Field—Three Z Axis]

Live Cell Spinning Disk Confocal Fluorescence Imaging of Cells- YFP and Bright Field Images - http://www.signaling-gateway.org/data/cgi-bin/ProtocolFile.cgi/afcs_PP00000145.pdf?pid=PP00000145

Category: Microscopy Protocols: Confocal Microscopy Protocols

Protocol describes the acquisition and processing of confocal fluorescent and bright field images of live cells expressing yellow fluorescent protein (YFP), with a spinning disk confocal head on a Zeiss Axiovert 200 M microscope. Protocol includes: Description of Microscope and Imaging Setup; Description of Acquisition Parameters; Image Processing. - [Read Live Cell Spinning Disk Confocal Fluorescence Imaging of Cells- YFP and Bright Field Images]

Live Cell Spinning Disk Confocal Fluorescence Imaging of Cells- YFP Time Series for Markers - http://www.signaling-gateway.org/data/cgi-bin/ProtocolFile.cgi/afcs_PP00000146.pdf?pid=PP00000146

Category: Microscopy Protocols: Confocal Microscopy Protocols

Protocol describes the acquisition and processing of confocal fluorescent images of live cells expressing yellow fluorescent protein (YFP), with a spinning disk confocal head on a Zeiss Axiovert 200 M microscope. Protocol includes: Description of Microscope and Imaging Setup; Description of Acquisition Parameters; Movie Processing. - [Read Live Cell Spinning Disk Confocal Fluorescence Imaging of Cells- YFP Time Series for Markers]

MTT Cell Proliferation Assay Protocol - http://www.atcc.org/pdf/30-1010k.pdf

Category: Cell Biology and Cell Culture: Cell Viability Protocols

The MTT Cell Proliferation Assay measures the cell proliferation rate and conversely, when metabolic events lead to apoptosis or necrosis, the reduction in cell viability. The number of assay steps has been minimized as much as possible to expedite sample processing. The MTT Reagent yields low background absorbance values in the absence of cells. Includes: Determining optimal cell counts, performing an assay, data interpretations and troubleshooting. - [Read MTT Cell Proliferation Assay Protocol]

Multiple-Target DNA In Situ Hybridization with Enzyme-Based Cytochemical Detection Systems Protocol - http://www.roche-applied-science.com/PROD_INF/MANUALS/InSitu/pdf/ISH_112-123.pdf

Category: Cytogenetics Protocols: In Situ Hybridization Protocols

Protocol for multiple-target DNA in situ hybridization with enzyme-based cytochemical detection systems. Includes: Cell preparations; Cell processing; Probe preparation; Multiple-target in situ hybridization (ISH); ISH with separate probe and target denaturation [for probes with repetitive (e.g., Alu) elements]; Post-hybridization washes; Enzyme-based cytochemical detection; etc.. - [Read Multiple-Target DNA In Situ Hybridization with Enzyme-Based Cytochemical Detection Systems Protocol]

Post-Processing of Arrays - http://cmgm.stanford.edu/pbrown/protocols/3_post_process.html

Category: DNA Microarray Protocols

Post-Processing of Arrays. Brown Lab. - [Read Post-Processing of Arrays]

Preparation and LCM of Paraffin Embedded Tissue Sections Protocol - http://dir.nichd.nih.gov/lcm/LCMTAP.htm#II.%20Preparation%20and%20LCM%20of%20Paraffin%20Embedded%20Tissue%20Sections

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

Protocol for the preparation of LCM of Paraffin embedded tissue sections. Includes: Fixation; Processing, Embedding and Tissue Sectioning; Staining; Laser Transfer; DNA Extraction Protocol of LCM tissue and PCR for DNA analysis; RNA Extraction Protocol of LCM tissue and RT-PCR for mRNA analysis. - [Read Preparation and LCM of Paraffin Embedded Tissue Sections Protocol]

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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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