probes Protocols

Category: BACs Bacterial Artificial Chromosome Protocols

Protocol presents the amplification of insert end sequences from bacterial artificial chromosome clones using TAIL-PCR. The amplified products are suitable as probes for chromosome walking and genome mapping and as templates for direct sequencing. The protocol has been used in rice genome studies. - [Read Amplification of Insert End Sequences from BACs Clones by Thermal Asymmetric Interlaced PCR]

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

The ability to synthesize RNA in the lab is critical to many techniques.Radiolabeled and nonisotopically labeled RNA probes, generated in small scale transcription reactions can be used in blot hybridizations and nuclease protection assays. This article includes information on: Requirements For Transcription, RNA Phage Polymerases, Template Options: Plasmids, PCR Products, Oligonuclotides and cDNA, Sense or Antisense, Conventional Or Large Scale Synthesis, Products for In Vitro Transcription. - [Read Basic Information on In Vitro Transcription]

Category: Cytogenetics Protocols: In Situ Hybridization Protocols

Choosing the right labeling method for your hybridization experiment. Includes: Homogeneous labeling methods for DNA; Homogeneous labeling methods for RNA; Stability of probe-target interaction; Nonradioactive labeling of oligonucleotides; Double-stranded versus single-stranded probes. - [Read Choosing the Right Labeling Method for your Hybridization Experiment]

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]

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]

Category: Cytogenetics Protocols: Fluorescent In Situ Hybridization FISH Protocol

Protocol for Detection (FISH). TRITC, or Avidin Cy-5. For the probes labeled with digoxigenin, we usually first incubate with mouse-anti-digoxigenin, followed by incubation with sheep anti-mouse Cy5.5, or other fluorochrome conjugated antibodies. - [Read Detection FISH Protocol]

Category: Drosophila Protocols: Drosophila Genetics Protocols

Protocol for detection of even-skipped transcripts in Drosophila embryos with PCR/DIG-labeled DNA probes. - [Read Detection of Even-Skipped Transcripts in Drosophila Embryos with PCR/DIG-Labeled DNA Probes]

Category: Cytogenetics Protocols: In Situ Hybridization Tissue Sections Protocols

Protocol for detection of even-skipped transcripts in drosophila embryos with PCR/DIG-labeled DNA probes. This protocol has been used to detect the transcript distribution of a number of genes by in situ hybridization, including evenskipped and seven-up, in whole mount Drosophila embryos, and engrailed Antennapedia in whole mount grasshopper embryos. Includes: Probe labeling; Evaluation of labeling reaction; Preparation of embryos, hybridization and detection.
 - [Read Detection of Even-Skipped Transcripts in Drosophila Embryos with PCR/DIG-Labeled DNA Probes Protocol]

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]

Category: Cytogenetics Protocols: In Situ Hybridization Tissue Sections Protocols

Protocol for detection of mRNA on paraffin embedded material of the central nervous system with DIG-labeled RNA probes. - [Read Detection of mRNA on Paraffin Embedded Material of the Central Nervous System with DIG-Labeled RNA]

Category: Cytogenetics Protocols: In Situ Hybridization Tissue Sections Protocols

Protocol for detection of mRNAs on cryosections of the cardiovascular system using DIG-labeled RNA probes. Protocol was optimized from a protocol using 35S-labeled RNA probes. It allows to detect the expression of low abundant mRNAs in the cardiovascular system, e.g. of the proinflammatory cytokine GM-CSF in normal human coronary arteries, and of IL6 and gp130 in human failing hearts. The protocol can be combined with immunohistochemistry. - [Read Detection of mRNAs on Cryosections of the Cardiovascular System Using DIG-Labeled RNA Probes]

Category: Cytogenetics Protocols: DIG Biotin Labeled Probe Protocols

Protocol for DIG labeling of cDNA probes. Includes: Incorporation DIG during PCR; Estimating the yield of DIG labeled probes; DNA Dot Blotting; Prehybridization and Hybridization. - [Read DIG Labeling of cDNA Probes Protocol]

Category: Nucleic Acid Modification Protocols: DIG Biotin Labeled Probes Protocols

Protocol for DIG labeling of cDNA probes. Includes: Incorporation DIG during PCR; Estimating the yield of DIG labeled probes; DNA Dot Blotting; Prehybridization and Hybridization. - [Read DIG Labeling of cDNA Probes Protocol]

Category: Cytogenetics Protocols: DIG Biotin Labeled Probe Protocols

Protocol describes here a high sensitivity indirect detection procedure for DIG-labeled hybridization probes. The procedure uses the components of the HNPP Fluorescent Detection Set to form a fluorescent precipitate of HNPP (2-hydroxy-3-naphthoic acid-2’-phenylanilide phosphate) and Fast Red TR at the site of hybridization. Includes: In situ hybridization with DIG-labeled probes; Detection of DIG-labeled probes; Fluorescence microscopy. - [Read DNA In Situ Hybridization with an Alkaline Phosphatase-Based Fluorescent Detection System]

Category: Nucleic Acid Modification Protocols: DIG Biotin Labeled Probes Protocols

Protocol describes a high sensitivity indirect detection procedure for DIG-labeled hybridization probes.  The procedure uses the components of the HNPP Fluorescent Detection Set to form a fluorescent precipitate of HNPP (2-hydroxy-3-naphthoic acid-2’-phenylanilide phosphate) and Fast Red TR at the site of hybridization.  This procedure can be used to detect single copy sequences as small as 1 kb on human metaphase chromosomes. 
    - [Read DNA In Situ Hybridization with an Alkaline Phosphatase-Based Fluorescent Detection System Protocol]

Category: E Coli Protocols: E coli Nucleic Acid Protocols

Protocol for E coli total RNA labeling for spotted microarray. Includes: RNA Preparation; Labeling; Clean up Labeled Probes. - [Read E.coli Total RNA Labeling Protocol for Spotted Microarray]

Category: Cytogenetics Protocols: Fluorescent In Situ Hybridization FISH Protocol

Protocol for fluorescence in situ hybridization (FISH) on human chromosomes and interphase nuclei. Includes: Plasmid probes; COSMID-, YAC- and LIBRARY PROBES; Probe detection. - [Read Fluorescence In Situ Hybridization (FISH) on Human Chromosomes and Interphase Nuclei Protocol]

Category: Nucleic Acid Modification Protocols: Nucleic Acid Labeling Protocols

Hybridization is carried out in conventional aqueous solvents at a temperature well below the predicted melting temperature.  Nonspecific hybrids are then removed by washing at high stringency in buffers containing quaternary salts.  Tetramethylammonium chloride (TMACl) is used with probes that are 14-50 nucleotides in length, whereas tetraethylammonium chloride (TEACl) is used with longer oligonucleotides. - [Read Hybridization of Oligonucleotide Probes in Aqueous Solutions Protocol]

Category: Immunology: Immunoprecipitation Protocols: Protein Immunoprecipitation Protocols

Protocol for the immunoprecipitation (IP) of Homer 1a, injection of virions and in situ hybridization in the spinal cord. Includes: Immunoprecipitation (IP) of Homer1a from spinal cord; Injection of virions in the parenchyma of the spinal dorsal horn in vivo; Generation of cRNA probes; Analysis of DIG-dUTP incorporation; Tissue hybridization. - [Read Immunoprecipitation of Homer 1a, Injection of Virions and In Situ Hybridization in the Spinal Cord]

Category: RNA Protocols: cDNA Libraries Library

Adsroption of Anti-E. coli Antibodies, cDNA Library Screening, Frank Lab. Oklahoma Medical Research Foundation - [Read Immunoscreening of Lambda-GT11 Bacteriophage Libraries with Antibody Probes]

Category: Cytogenetics Protocols

In situ hybridisation to alpha satellite sequences (chromosome specific). Method book .net - [Read In situ hybridisation to alpha satellite sequences (chromosome specific)]

Category: Cytogenetics Protocols: DIG Biotin Labeled Probe Protocols

In situ hybridisation to alpha satellite sequences (chromosome specific) protocol. - [Read In Situ Hybridisation to Alpha Satellite Sequences (Chromosome Specific) Protocol]

Category: Nucleic Acid Modification Protocols: DIG Biotin Labeled Probes Protocols

Protocol for in situ hybridisation to alpha satellite sequences (chromosome specific). - [Read In Situ Hybridisation to Alpha Satellite Sequences Protocol]

Category: Cytogenetics Protocols: DIG Biotin Labeled Probe Protocols

Protocol for In situ hybridization to human metaphase chromosomes using DIG-, biotin-, or fluorochrome-labeled DNA probes and detection with fluorochrome conjugates. Includes: Pretreatment of metaphase spreads on slides; Denaturation and hybridization; Single color fluorescent detection with immunological amplification; Multicolor fluorescence in situ hybridization (Multicolor FISH); Results obtained with human metaphase chromosome spreads. - [Read In Situ Hybridization to Human Metaphase Chromosomes using DIG-, Biotin- or Fluorochrome-Labeled DNA]

Category: Nucleic Acid Modification Protocols: DIG Biotin Labeled Probes Protocols

Protocol for in situ hybridization to human metaphase chromosomes using DIG-, biotin-, or fluorochrome-labeled DNA probes and detection with fluorochrome conjugates. - [Read In Situ Hybridization to Human Metaphase Chromosomes Using DIG-, Biotin-, or Fluorochrome-Labeled]