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S1 Nuclease Analysis Protocol - http://www.flemingtonlab.com/Protocols/S1NucleaseProtocol.pdf

Category: Molecular Biology Protocols

Protocol for S1 nuclease analysis. - [Read S1 Nuclease Analysis Protocol]

Sample Labeling for Microarray Analysis - http://research.nhgri.nih.gov/microarray/sample_labeling.shtml

Category: DNA Microarray Protocols

Reverse transcription labeling using Cy3 and Cy5. Sample Labeling for Microarray Analysis. NHGRI - [Read Sample Labeling for Microarray Analysis]

Serial Analysis Of Gene Expression (SAGE) - http://www.embl-heidelberg.de/info/sage/

Category: Genetics and Genomics: Cancer Genetics Protocols

SAGE is a new method that has been invented at Johns Hopkins University in USA to give scientists an overview of a cell’s complete gene activity. It works by capturing RNAs, identifying them and counting them. By comparing different types of cells, the researchers hope to generate profiles that will help them understand healthy cells and what goes wrong during diseases. Includes: How SAGE works and Steps of SAGE. - [Read Serial Analysis Of Gene Expression (SAGE)]

Simultaneous Analysis of DNA Content and Surface Immunophenotype Protocol - http://www.cyto.purdue.edu/flowcyt/research/cytotech/telford/ethanol.htm

Category: Cell Biology and Cell Culture: Flow Cytometry Protocols: DNA Staining Protocols for Flow Cytometry

In an attempt to accurately measure DNA content with simultaneous preservation of cell surface markers, we have utilized gentle ethanol treatment techniques, which permeablize cells with minimal loss of surface antigen expression and antibody-antigen association. For some cell types, the presence of apoptotic cells based on reduced DNA content can also be detected. One such technique employs the addition of ethanol to cells previously resuspended in high concentrations of fetal bovine serum... - [Read Simultaneous Analysis of DNA Content and Surface Immunophenotype Protocol]

Singel Nucleotide Primer Extension (SNuPE) - http://www.methods.info/Methods/DNA_methylation/SNuPE.html

Category: Epigenetics and Methylation Protocols: Bisulfite Treatment Methylation Assay Protocol

Single Nucleotide Primer Extension can be used for the analysis of methylation in a certain position. Treat DNA with bisulphite and then anneal a primer which ends immediately before the site of analysis. Dr. A. Gratchev Methods.info - [Read Singel Nucleotide Primer Extension (SNuPE)]

SINGLE CELL CAPTURE AND ANALYSIS - http://dir.nichd.nih.gov/lcm/sin_cell_collection.htm

Category: Histology Protocols: Laser Capture and Microdissection

SINGLE CELL CAPTURE AND ANALYSIS. NIH LASER CAPTURE MICRODISSECTION PROTOCOLS. Protocol for Laser Capture Microdissection. - [Read SINGLE CELL CAPTURE AND ANALYSIS]

Single Colour Fish Analysis Method - http://www.sanger.ac.uk/HGP/methods/cytogenetics/single_colour.shtml

Category: Cytogenetics Protocols: Fluorescent In Situ Hybridization FISH Protocol

Single colour detection for biotinylated probes. Sanger Institute - [Read Single Colour Fish Analysis Method]

Single-Strand Conformation Polymorphism Analysis Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/14/pdb.prot4118

Category: Genetics and Genomics: Cancer Genetics Protocols: Single Strand Conformational Polymorphism(SSCP) Protocols

Single-strand confirmation polymorphism analysis (SSCP) is a powerful and robust method for the detection of DNA sequence changes (single-base substitutions) based on shifts in electrophoretic mobility. In this protocol, the target sequence is simultaneously labeled and amplified, then heat-denatured and resolved by non-denaturing polyacrylamide gel electrophoresis. - [Read Single-Strand Conformation Polymorphism Analysis Protocol]

Single-Strand Conformation Polymorphism Analysis Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/14/pdb.prot4118

Category: DNA Protein Interactions Protocols: Electrophoretic Mobility Shift Assays EMSA Protocols

The target sequence is simultaneously labeled and amplified, then heat-denatured and resolved by non-denaturing polyacrylamide gel electrophoresis. Differences in sequence alter the conformation of the DNA and hence its electrophoretic mobility and, because of the high resolution of polyacrylamide gels, most conformational changes caused by subtle changes in sequence can be detected. - [Read Single-Strand Conformation Polymorphism Analysis Protocol]

Single-tube Coupled Transcription/Translation Reactions for Eukaryotic In Vitro - http://www.promega.com/tbs/tm045/tm045.pdf

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

Information for protocol using single-tube, coupled transcription/translation reactions for eukaryotic in vitro translation. Includes information on: Translation Procedure; Positive Control Translation Reactions Using Luciferase; Cotranslational Processing Using Canine Pancreatic Microsomal Membranes; Post-Translational Analysis; Positive Control Luciferase Assays; Composition of Buffers and Solutions; Luciferase SP6/T7 Control DNAs - [Read Single-tube Coupled Transcription/Translation Reactions for Eukaryotic In Vitro]

Site-Specific Protein-DNA Photo-Cross-Linking: Analysis of Structural Organization of Protein-DNA - http://www.cshprotocols.org/cgi/content/abstract/2006/29/pdb.prot4588

Category: DNA Protein Interactions Protocols

The multiprotein-DNA complex of interest is formed using the site-specifically derivatized DNA fragment. The complex is then UV-irradiated, initiating covalent cross-linking with proteins in direct physical proximity to the cross-linking agent. Extensive nuclease digestion is performed to eliminate uncross-linked DNA and convert cross-linked DNA to a cross-linked, radiolabeled nucleotide "tag." - [Read Site-Specific Protein-DNA Photo-Cross-Linking: Analysis of Structural Organization of Protein-DNA]

Slide Preparation for Laser Capture Microdissection (LCM) Protocol - http://cgap-mf.nih.gov/Protocols/Slides/SlideProtocols/SlidePrepforLCM.html

Category: Primary Cell Isolation and Culture Protocols: Laser Capture Microdissection Protocols: Tissue Preparation for LCM Protocols

Protocol for slide preparation for laser capture microdissection (LCM) for subsequent DNA, RNA, and protein analysis. - [Read Slide Preparation for Laser Capture Microdissection (LCM) Protocol]

Slide Preparation for Manual Microdissection Protocol - http://cgap-mf.nih.gov/Protocols/Slides/SlideProtocols/SlidePrepManualMicrodissection.html

Category: Primary Cell Isolation and Culture Protocols

Slide Preparation for Manual Microdissection for Subsequent DNA, RNA, and Protein Analysis. Manual microdissection and subsequent molecular analysis can be carried out on slides stained using standard hematoxylin and eosin methods. However, if cell types that are (or are not) expressing a specific protein are required for a study, then more advanced slide preparation methods such as Immuno-LCM may be utilized. - [Read Slide Preparation for Manual Microdissection Protocol]

Small Scale DNA Preps for Neurospora crassa Protocol - http://www.fgsc.net/fgn/irelan.html

Category: Fungi Protocols: Neurospora Protocols

DNA isolation method yields an average of 0.6 micrograms of genomic DNA that is suitable for Southern analysis or PCR. Starting with fresh mycelium, 20 to 40 samples can be processed in approximately two hours. Better yields (about 5 micrograms) may be obtained by suspending approximately 100 microliters of ground lyophilized mycelium in 500 microliters of isolation buffer and following the protocol. - [Read Small Scale DNA Preps for Neurospora crassa Protocol]

SNP Analysis and Presentation in the Pharmacogenetics of Membrane Transporters Project - http://psb.stanford.edu/psb-online/proceedings/psb03/stryke.pdf

Category: DNA Protocols: SNP Protocols

SNP Analysis and Presentation in the Pharmacogenetics of Membrane Transporters Project. DOUG STRYKE et al. PDF - [Read SNP Analysis and Presentation in the Pharmacogenetics of Membrane Transporters Project]

SNP detection with mutagenic primers - http://insilico.ehu.es/restriction/mutation_seq/

Category: DNA Protocols: SNP Protocols

SNP detection with mutagenic primers. Input sequence will be searched to find changes in one nucleotide near the location of the SNP, so that mutagenic primers may be easily designed. Bikandi, J., San MillÃ¡n, R., Rementeria, A., and Garaizar, J. In silico analysis of complete bacterial genomes: PCR, AFLP-PCR, and endonuclease restriction. Bioinformatics 2004 Mar 22;20(5):798-9. - [Read SNP detection with mutagenic primers]

Sodium and Potassium Analysis by Flow Cytometry Protocol - http://www.niehs.nih.gov/research/atniehs/core/fc/protocols/sodium.cfm

Category: Cell Biology and Cell Culture: Flow Cytometry Protocols

Protocol for sodium and potassium analysis by flow cytometry. Includes: Preparation of the dyes; Loading of the dyes; Flow Cytometric Analysis. - [Read Sodium and Potassium Analysis by Flow Cytometry Protocol]

Sodium and Potassium Analysis by Flow Cytometry Protocol - http://www.niehs.nih.gov/research/atniehs/core/fc/protocols/sodium.cfm

Category: Cell Biology and Cell Culture: Flow Cytometry Protocols: Intracellular Ion Measurement Protocols

Sorting Aberrant Cells Using Anti-Cytokeratin or DNA Content for Study of Cell Morphology - http://www.bdbiosciences.com/pdfs/whitePapers/23-2786-02.pdf

Category: Cell Biology and Cell Culture: Flow Cytometry Protocols: Cell Sorting Protocols

Demonstrates the use of the FACSort for sorting based on DNA ploidy or the presence of cytokeratin, and the suitability of the sorted cells for morphologic analysis by microscopic examination. - [Read Sorting Aberrant Cells Using Anti-Cytokeratin or DNA Content for Study of Cell Morphology]

Split Luciferase Complementation Assay for Studying Interaction of Proteins X and Y in Living Mice - http://www.cshprotocols.org/cgi/content/abstract/2006/29/pdb.prot4595

Category: Reporter Gene Assays: Luciferase Assay Protocols

Protocol describes a split luciferase complementation assay that can be used to repetitively and noninvasively study the interaction of proteins in small living animals. After the expression of the appropriate vectors has been checked in cell culture in vivo, studies can be performed either by implanting transiently transfected cells for short-term analysis (maximum of 7 days), or with tumor models grown from tumor cells stably expressing the complete reporter system. - [Read Split Luciferase Complementation Assay for Studying Interaction of Proteins X and Y in Living Mice]

Staining of Tissue Slices for Analysis of Axonal Pathfinding in dsRNA-Treated Avian Embryos - http://www.cshprotocols.org/cgi/content/abstract/2006/23/pdb.prot4507

Category: RNAi Technology Protocols: RNAi Avian Embryos Protocols

Protocol describes a method to stain nerve fibers in tissue slices of avian embryos using an antibody against the 160-kD subunit of neurofilaments. This allows the comparison of the branching pattern of motor and sensory neurons between control and experimental embryos. The tissue is cut in slices using a vibratome or tissue slicer. The protocol is suitable for older embryos after approximately stage 33 and regions that are not accessible by whole-mount analysis. - [Read Staining of Tissue Slices for Analysis of Axonal Pathfinding in dsRNA-Treated Avian Embryos]

Staining of Tissue Slices for Analysis of Axonal Pathfinding in dsRNA-Treated Avian Embryos Protocol - http://www.cshprotocols.org/cgi/content/abstract/2006/23/pdb.prot4507

Category: Avian Bird Protocols

Staining of Tissue Slices for Analysis of Axonal Pathfinding in dsRNA-Treated Avian Embryos Protocol - http://www.cshprotocols.org/cgi/content/abstract/2006/23/pdb.prot4507

Category: Neuroscience Protocols: Neuronal Stains Protocols

Protocol for staining of tissue slices for analysis of axonal pathfinding in dsRNA-treated avian embryos. - [Read Staining of Tissue Slices for Analysis of Axonal Pathfinding in dsRNA-Treated Avian Embryos Protocol]

Subcloning Analysis Protocol - http://stemcells.nih.gov/research/NIHresearch/scunit/subcloning.asp

Category: Stem Cell Protocols: Stem Cell Culture Protocols

Protocol for subcloning analysis. Includes cell lines: BG01(1), TE03, TE06, UC06(1), WA01, WA07, WA09. - [Read Subcloning Analysis Protocol]

Targeted Differential Display Protocol - http://cgap-mf.nih.gov/Protocols/DNARNAProteomicAnalysis/RNA/TargetedDifferentialDisplay.html

Category: Primary Cell Isolation and Culture Protocols

The protocol is one example of differential gene expression analysis of cells obtained from microdissected tissue. Includes: Microdissection and RNA Isolation; Reverse Transcription; PCR; P.A.G.E.; Sequencing of Differentially Expressed Bands. - [Read Targeted Differential Display Protocol]

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Populational Analysis of Genomic DNA Protocol

A protocol on the populational Analysis of genomic DNA.

In Vitro Translated Xenopus Mos Kinase Assay Protocol

In Vitro Translated Xenopus Mos Kinase Assay Protocol. In response to progesterone, immature Xenopus oocytes mature to eggs that can be fertilized. The Mos protein kinase is essential for oocyte maturation, most likely due to its ability to activate the MAP kinase cascade. This MAP kinase cascade eventually leads to the activation of Cdc2/cyclin B and entry into M phase. In this protocol, tagged Mos kinase is translated in vitro, immunopurified, and used in a kinase assay.

Absorption Spectroscopy and Quantification of Filamentous Phage Protocol

Unlike spherical phage, such as T4 and λ, which have roughly equal weight ratios of protein to DNA, filamentous phage have about six times more protein than DNA; the protein therefore contributes substantially to the absorption spectrum.

3' Rapid Amplification of cDNA Ends RACE Using PCR Protocol

3' Rapid Amplification of cDNA Ends RACE Using PCR Protocol. This protocol contains the steps for 3' end rapid amplification of mRNA by PCR. The first-strand cDNA is synthesized from total or poly(A+) RNA by priming from the poly-A tail of the mRNA using a oligo (dT) adaptor primer. The cDNA is then amplified via PCR using a gene-specific primer and an adaptor primer.

Toluidine Blue Stain

Toluidine Blue staining method and protocol for cell or tissue histology.

Thionin Stain

Thionin staining method and protocol for cell or tissue histology.

Picking Transfected ES Cell Clones Protocol

This protocol a protocol on how to generate transfected embryonic stem (ES) cell clones. The previous protocol in this series is the Protocol for Electroporation of ES cells. The next protocol in the series is the Protocol on Disaggregation, Expansion, and Freezing of Transfected ES Clones.

Vector Design Protocol for Transgenic Mice Generation

The protocol gives general considerations for the design of targeting vectors for transgenic mice. The protocol shares tips in the design of knock-out and knock-in vectors and some of their strategies for producing homologously recombined embryonic stem cells.

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