scanning 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: Molecular Biology Protocols: Carbohydrate Protocols

Characterization of Protein Glycosylation Using Chip-Based Nanoelectrospray with Precursor Ion Scanning Quadrupole Linear Ion Trap Mass Spectrometry. Sheng Zhang1 and Brian L. Williamson. Journal of Biomolecular Techniques, 16:209-219 2005. - [Read Characterization of Protein Glycosylation Using Chip-Based Nanoelectrospray with Precursor Ion Scann]

Category: Microscopy Protocols: Confocal Microscopy Protocols

There are two major forms of laser scanning microscopy: confocal laser scanning microscopy (CLSM) and multiphoton laser scanning microscopy (MPLSM). Information on: X-t scans and X-Y scans; Confocal Laser Scanning Microscopy; Multiphoton Laser Scanning Microscopy; MPLSM requires no pin hole; Advantages of MPLSM over CLSM. - [Read Confocal Laser Scanning Microscopy]

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

Flow Cytometry Analysis Protocol. Springer Lab - Harvard. Background on flow cytometry technique: Flow cytometry is a method which uses instrumentation scanning single cells flowing past excitation sources in a liquid medium.
- [Read Flow Cytometry Analysis Protocol]

Category: DNA Microarray Protocols

Preparation of Fluorescent DNA Probe from HUMAN mRNA or Total RNA using Direct Incorporation Washing and Scanning Arrays. Brown Lab. - [Read Human DNA Microarray Hybridization]

Category: Microarray Protocols: Microarray Hybridization Protocols

Protocol for hybridization to a scanning array made on glass. - [Read Hybridization to a Scanning Array Made on Glass Protocol]

Category: Microscopy Protocols: Electron Microscopy Protocols

The scanning transmission electron microscope precision and reproducibility of mass measurements are comparable with those of the analytical ultracentrifuge, the possibility of determining the mass not only of entire supramolecular assemblies but also of their distinct components has opened exciting new avenues which have occasionally been entered but are not yet fully explored. Includes: Principle and application (The GroEL:GroES complex). - [Read Imaging and Measuring Biomolecules & Their Assemblies by Scanning Transmission Electron Microscopy]

Category: Microscopy Protocols: Electron Microscopy Protocols

In recent years, the increased sensitivity of electron detectors and the availability of low-vacuum or variable-pressure systems have allowed imaging of fresh tissue samples without the need for fixation, drying, and coating. This obviously saves a lot of time, although the image quality may not be as good as that obtained from fixed samples. However, for most applications that tend to be at a relatively low magnification, the quality can be as good as that obtained from fixed samples. - [Read Imaging of Fresh Arabidopsis Tissues in the Scanning Electron Microscope]

Category: Plant Biology Protocols

In recent years, the increased sensitivity of electron detectors and the availability of low-vacuum or variable-pressure systems have allowed imaging of fresh tissue samples without the need for fixation, drying, and coating. This obviously saves a lot of time, although the image quality may not be as good as that obtained from fixed samples. However, for most applications that tend to be at a relatively low magnification, the quality can be as good as that obtained from fixed samples. - [Read Imaging of Fresh Arabidopsis Tissues in the Scanning Electron Microscope Protocol]

Category: Microscopy Protocols: Live-Cell Imaging Protocols

Using confocal laser-scanning microscope & GFP fusion proteins in time-lapse imaging to visualize the behavior of organelles and to track membrane-bound transport intermediates that bud off from organelles. Practical issues related to construction & expression of GFP fusion proteins are discussed. Essential for optimizing the brightness and expression levels of GFP fusion proteins so that intracellular membrane-bound structures containing these fusion proteins can be readily visualized. - [Read Imaging of Organelle Membrane Systems and Membrane Traffic in Living Cells]

Category: Microscopy Protocols: In Vivo Imaging Protocols

Positron emission tomography (PET) is a established quantitative and noninvasive imaging modality. With the PET reporter gene (PRG)/PET reporter probe (PRP) system, based on a mutant form of herpes simplex virus 1 thymidine kinase (HSV1-sr39tk), the PET signal is directly proportional to the enzymatic activity of sr39TK9-14. In this protocol, we describe in detail a method for reporter gene labeling of islets and quantitative scanning using a reporter probe. - [Read In Vivo Functional Real-Time Imaging of Transplanted Islets Using Positron Emission Tomography (PET)]

Category: Microscopy Protocols: Confocal Microscopy Protocols

Information on: Applications of Confocal Microscopy; Practical Instruments; Limitations of point-scanning Confocal Microscopy; Parallel beam confocal Imaging Systems. - [Read Information on Confocal Imaging]

Category: Microscopy Protocols: Confocal Microscopy Protocols

Confocal laser scanning microscopy (CLSM) is a relatively new light microscopical imaging technique which has found wide applications in the biological sciences. The primary value of the CLSM to the biologist is its ability to produce optical sections through a 3-D specimen-e.g., an entire cell or a piece of tissue - that, to a good approximation, contain information from only one focal plane. Article includes principle and applications of confocal laser scanning microscope. - [Read Looking Inside Cells and Tissues by Optical Sectioning with a Confocal Laser Scanning Microscope]

Category: DNA Microarray Protocols

Making a scanning array: in situ synthesis of oligonucleotides on a solid substrate. Elder et al., Oxford Practical Approach Series. - [Read Making a scanning array: in situ synthesis of oligonucleotides on a solid substrate]

Category: Microscopy Protocols: Optical Microscopy Protocols

Diffraction-limited optical microscopy requires that the spatial resolution of an image is limited by the wavelength of the incident light & by the numerical apertures of the condenser & objective lens systems.The development of near-field scanning optical microscopy (scanning near-field optical microscopy) has allowed for a imaging technique that retains the various contrast mechanisms afforded by optical microscopy methods while attaining spatial resolution beyond the optical diffraction limit - [Read Near-Field Scanning Optical Microscopy]

Category: Microscopy Protocols: Optical Microscopy Protocols

Near-field scanning optical microscopy can achieve spatial resolution performance beyond the classical diffraction limit by employing a sub-wavelength light source or detector positioned in close proximity to a specimen. Such a sub-wavelength source usually consists of an aperture at the end of a tapered probe, which functions basically as a wave guide. Includes info.: Fiber Probe Fabrication; Pulling Method; Meniscus Etching; Selective Etching; Apertureless and Alternative Probe Designs etc. - [Read Near-Field Scanning Optical Microscopy: NSOM Probes]

Category: Nucleic Acid Detection Protocols

Protocol for preparation of fluorescent DNA probe from HUMAN mRNA or total RNA using direct incorporation. Includes: Preparing fluoresenctly labeled cDNA (probe); Washing and Scanning Arrays. - [Read Preparation of Fluorescent DNA Probe from HUMAN mRNA or Total RNA using Direct Incorporation]

Category: Microarray Protocols: Microarray Hybridization Protocols

Protocol for the preparation of fluorescent DNA probe from HUMAN mRNA or total RNA using direct incorporation. Includes: Preparing fluoresenctly labeled cDNA (probe); Washing and Scanning Arrays. - [Read Preparation of Fluorescent DNA Probe from HUMAN mRNA/ Total RNA using Direct Incorporation Protocol]

Category: DNA Microarray Protocols

Reverse transcriptase labeling with Cy3/Cy5, Staining of total DNA on slides, construction, Laser scanning, Spot quantitation, Statistics, sample tracking. Vodkin Laboratory. U.Illinois. - [Read Protocols for microarray development in use in the Vodkin Laboratory]

Category: Nucleic Acid Detection Protocols

Restriction landmark genomic scanning (RLGS) is a method to detect large numbers of restriction landmarks in a single experiment.  It is based on the concept that restriction enzyme sites can serve as landmarks throughout a genome.  RLGS uses direct end-labeling of the genomic DNA digested with a rare-cutting restriction enzyme and high-resolution two-dimensional electrophoresis. - [Read Restriction Landmark Genomic Scanning Protocol]