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Methylation and Epigenetics Bioinformatic Tools - http://www.molecularstation.com/bioinformatics/link/Epigenetics_and_Methylation/

Category: Epigenetics and Methylation Protocols

Methylation database, CpG Island predictors, Methylation Primer design tools and databases. Epigenetic tools and bioinformatics. - [Read Methylation and Epigenetics Bioinformatic Tools]

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Near-Field Scanning Optical Microscopy - http://microscopy.fsu.edu/primer/techniques/nearfield/nearfieldintro.html

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]

Near-Field Scanning Optical Microscopy: NSOM Probes - http://microscopy.fsu.edu/primer/techniques/nearfield/nearfieldprobes.html

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]

Nuclear Extract in vitro Transcription System - http://www.promega.com/tbs/tb123/tb123.pdf

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

Protocol describes a system which includes all of the necessary components for in vitro transcription as well as a positive control template that provides run-off transcripts from a CMV immediate early promoter. This system is designed for runoff transcription. Alternatively, transcription products can be analyzed by primer extension. - [Read Nuclear Extract in vitro Transcription System]

Oligonucleotide Details for PCR - http://sequence-www.stanford.edu/group/yeast_deletion_project/Primer_specs.html

Category: Yeast Protocols: Yeast Nucleic Acid Protocols: Yeast PCR Protocols

Information for oligonucleotide details required for PCR. Includes: Primer choice; UPTAG PRIMER; DNTAG PRIMER; UP_45 and DOWN_45 PRIMERS; UP_90 and DOWN_90 PRIMERS. - [Read Oligonucleotide Details for PCR]

One-Step Isolation of Plant DNA Suitable for PCR Amplification - http://pubs.nrc-cnrc.gc.ca/ispmb/ispmb19/r01-054.pdf

Category: Plant Biology Protocols: Plant DNA RNA Isolation Protocols

One step extraction for isolation of plant DNA. DNA suitable for amplification by PCR can be produced from leaf material smaller than 0.3 mm2 in less than 20 min & no tube changes. Method was tested on several plant species. Method was found to extract DNA that could be amplified without any further purification or treatment. The isolated DNA was amplified using a universal chloroplast primer set. The method was validated by comparing size of PCR products generated using standard DNA isolation. - [Read One-Step Isolation of Plant DNA Suitable for PCR Amplification]

Optimal Microscopy Primer - Molecular Expressions - http://micro.magnet.fsu.edu/primer/digitalimaging/index.html

Category: Molecular Imaging

Optimal Microscopy Primer - Molecular Expressions. Introduces most microscopy techniques - [Read Optimal Microscopy Primer - Molecular Expressions]

PCR and Multiplex Guide - http://info.med.yale.edu/genetics/ward/tavi/Guide.html

Category: DNA Protocols: PCR Polymerase Chain Reaction Protocols: PCR Optimization Protocols

A Great PCR and Multiplex Guide. Topics for PCR optimization. Primer conditions, PCR temperatures, etc. Octavian Henegariu. - [Read PCR and Multiplex Guide]

PCR and Multiplex Guide - http://info.med.yale.edu/genetics/ward/tavi/Guide.html

Category: DNA Protocols: PCR Polymerase Chain Reaction Protocols: Standard PCR Protocol

PCR and Multiplex Guide. Amazing Guide to primer amount, MgCl2 amount, annealing temperature, and more. With picture examples. Octavian Henegariu. - [Read PCR and Multiplex Guide]

PCR and Multiplex Guide - http://info.med.yale.edu/genetics/ward/tavi/Guide.html

Category: PCR Protocols: PCR Optimization

A Great PCR and Multiplex Guide. Topics for PCR optimization. Primer conditions, PCR temperatures, etc. Octavian Henegariu. - [Read PCR and Multiplex Guide]

PCR and Multiplex Guide - http://info.med.yale.edu/genetics/ward/tavi/Guide.html

Category: PCR Protocols: Standard PCR Protocol

PCR and Multiplex Guide. Amazing Guide to primer amount, MgCl2 amount, annealing temperature, and more. With picture examples. Octavian Henegariu. - [Read PCR and Multiplex Guide]

PCR Genotyping from Tail DNA Protocol - http://genetics.med.harvard.edu/~cepko/protocol/mike/P4.html

Category: Genetics and Genomics: Genotyping Protocols: PCR Genotyping

Protocol for PCR genotyping from tail DNA. This protocol works well for a variety of genes and primer pairs including Tg and KO alleles. Oligonucleotide melting temperatures between 60° and 65° seem to work well. - [Read PCR Genotyping from Tail DNA Protocol]

PCR Genotyping Primer Pairs Protocols - http://mgc.wustl.edu/protocols/pcr_primer_set.html

Category: Genetics and Genomics: Genotyping Protocols: PCR Genotyping

Primer pairs will amplify sequences present as a single copy in the mouse genome with the Universal Genotyping Protocol. Includes: b-Galactosidase (LacZ); cre-recombinase; CFP; diphtheria toxin; dsRED; Fabpi-200; Fabpi-500; flp recombinase; GFP/BFP/YFP; human growth hormone (complete); human growth hormone (transcriptional stop); luciferase (click-beetle); luciferase (firefly); neomycin phosphotransferase; SRY (male-specific); tTA (tet-on). - [Read PCR Genotyping Primer Pairs Protocols]

PCR primer design and pcr reaction optimization. - http://www.mcb.uct.ac.za/pcroptim.htm

Category: PCR Protocols: PCR Optimization

PCR primer design and pcr reaction optimization. Ed Rybicki. Factors Affecting the PCR, Denaturing Temperature and Time, Annealing Temperature and Primer Design, Primer Length, Degenerate Primers, Elongation , Temperature and Time, Reaction Buffer, Cycl - [Read PCR primer design and pcr reaction optimization.]

PCR PRIMER DESIGN AND REACTION OPTIMISATION: Molecular Biology Techniques Manual - http://www.mcb.uct.ac.za//pcroptim.htm

Category: DNA Protocols: PCR Polymerase Chain Reaction Protocols: PCR Optimization Protocols

PCR PRIMER DESIGN AND REACTION OPTIMISATION: Molecular Biology Techniques Manual - Rybicki - [Read PCR PRIMER DESIGN AND REACTION OPTIMISATION: Molecular Biology Techniques Manual]

PCR PRIMER DESIGN AND REACTION OPTIMISATION: Molecular Biology Techniques Manual - http://www.mcb.uct.ac.za//pcroptim.htm

Category: PCR Protocols: PCR Optimization

PCR PRIMER DESIGN AND REACTION OPTIMISATION: Molecular Biology Techniques Manual - Rybicki - [Read PCR PRIMER DESIGN AND REACTION OPTIMISATION: Molecular Biology Techniques Manual]

PCR-Mediated Gene Disruption: One-Step Method Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/1/pdb.prot4169

Category: PCR Protocols

DNA prepared by PCR-mediated gene disruption can be used to transform yeast in gene replacement experiments. This protocol uses two primers, tailed with approximately 50 nucleotides homologous to the gene of interest, that target insertion of the PCR product to that locus. Each primer ends with a universal sequence that is designed to amplify various selectable markers from plasmid templates. - [Read PCR-Mediated Gene Disruption: One-Step Method Protocol]

Precision Engineering of Plant Gene Loci by Homologous Recombination Cloning in Escherichia Coli - http://www.plantmethods.com/content/1/1/6

Category: Plant Biology Protocols: Arabidopsis Genetics Protocols

Protocol for precision engineering of plant gene loci by homologous recombination cloning in Escherichia coli. Includes: Key steps in the EL250 RED-HR locus rescue and engineering procedure; Primer design and plasmid constructs; AtSTM gap-repair construct; Targeting construct backbone; Preparation of electrocompetent EL250 cells; Transformation of BAC F24o1 and induction of recombinogenic function in EL250; AtSTM locus rescue from BAC F24o1 by gap-repair HR. - [Read Precision Engineering of Plant Gene Loci by Homologous Recombination Cloning in Escherichia Coli]

Preparing Denatured Templates for Sequencing by Dideoxy-mediated Chain Termination Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/2/pdb.prot3787

Category: DNA Protocols: DNA Sequencing Protocols: Dideoxy Mediated Sequencing Protocols

Protocol describes how double-stranded plasmid DNA is denatured byalkali and annealed to an appropriate oligonucleotide primer,in preparation for dideoxy-sequencing reactions catalyzed bySequenase. - [Read Preparing Denatured Templates for Sequencing by Dideoxy-mediated Chain Termination Protocol]

Random Amplification of Polymorphic DNA (RAPD) Typing and Fingerprinting Protocol - http://www.aspergillus.org.uk/indexhome.htm?secure/laboratory_protocols/./rapds.html~main

Category: Fungi Protocols: Aspergillus Protocols

RAPD is a procedure for typing and fingerprinting isolates of a species. It can be used for epidemiological studies, such as investigations into hospital outbreaks and as a laboratory aid to keep track of cultures and to verify that mutants generated in the laboratory are genetically identical to the parental strain. In our hands, the use of one primer, R108, is sufficiently discriminatory to distinguish between the isolates of different strains. - [Read Random Amplification of Polymorphic DNA (RAPD) Typing and Fingerprinting Protocol]

Random Primer DNA Labeling Protocol - http://www.flemingtonlab.com/Protocols/RandomPrimerLabeling.pdf

Category: Nucleic Acid Modification Protocols: Random Primer Labeling Protocols

Protocol for random primer DNA labeling. - [Read Random Primer DNA Labeling Protocol]

Random Primer Labeling of PolyA and RNA Protocol - http://molbiol.ru/eng/protocol/23_01.html

Category: Nucleic Acid Modification Protocols: Random Primer Labeling Protocols

Protocol for random primer labeling of poly A and RNA. Includes: Random primer reaction; cDNA purification; Hybridization; Washing; Stripping of membranes. - [Read Random Primer Labeling of PolyA and RNA Protocol]

Rapid Amplification of 3' cDNA Ends 3'-RACE Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/2/pdb.prot3865

Category: PCR Protocols: cDNA Synthesis Protocols

3'-RACE reactions are used to isolate unknown 3' sequences or to map the 3' termini of mRNAs onto a gene sequence. 3'-RACE requires knowledge of a small region of sequence within either the target RNA or a partial clone of cDNA. A population of mRNAs is transcribed into cDNA with an adaptor-primer consisting at its 3' end of a poly(T) tract and at its 5' end of an arbitrary sequence of 30-40 nucleotides. - [Read Rapid Amplification of 3' cDNA Ends 3'-RACE Protocol]

Rapid Amplification of 5' cDNA Ends 5'-RACE Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/2/pdb.prot3989

Category: PCR Protocols: cDNA Synthesis Protocols

This method is used to extend partial cDNA clones by amplifying the 5' sequences of the corresponding mRNAs. The technique requires knowledge of a small region of sequence within the partial cDNA clone. During PCR, the thermostable DNA polymerase is directed to the appropriate target RNA by a single primer derived from the region of known sequence. - [Read Rapid Amplification of 5' cDNA Ends 5'-RACE Protocol]

Real-Time or Kinetic PCR - http://dna-9.int-med.uiowa.edu/realtime.htm

Category: Real Time PCR

Real-Time Chemistry, Instrumentation, Real-Time PCR Quantitation, Quantitative Primer and Probe Design, Thermal Cycling Parameters, Sample Preparation, and Real-time Data Analysis. - [Read Real-Time or Kinetic PCR]

Real-Time PCR (qPCR) Basics - http://web.archive.org/web/20040711051207/http://primerdesign.co.uk/primerdesign/qPCR_basics.html

Category: Real Time PCR

Learn Quantitative PCR Methodology. Assay parameters, Melt Curves and Primer Dimers, Standard Curves, Dynamic Range, Quantification methods, Delta CT, Standard Curves. Dr.Powell. - [Read Real-Time PCR (qPCR) Basics]

Articles (1-4 of 4)

Populational Analysis of Genomic DNA Protocol

A protocol on the populational Analysis of genomic DNA.

Genomic DNA Labeling of Microarrays Protocol

DNA microarrays are an ordered arrangement of DNA molecules complementary to genes of interest that are "spotted" by robotic equipment onto a glass slide substrate. The expression of genes in cells can be monitored with microarrays by preparing cDNA from the mRNA of cells of interest and measuring the hybridization to the microarray. This protocol describes the labeling of genomic DNA for use as a probe for hybridization to the cDNA spotted on the array.

Microarray Protocol Preparation of Fluorescent DNA Probes from Human mRNA

This Microarray Protocol Preparation of Fluorescent DNA Probes from Human mRNA protocol describes the production of probes labeled with the fluorescent dyes, Cy3 and Cy5, following the synthesis of cDNA from human mRNA and the hybridization of the probes to DNA microarrays.

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.

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