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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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Analysis of protein phosphorylation: methods and strategies PDF - http://www.blackwell-synergy.com/doi/pdf/10.1111/j.1365-313X.2005.02613.x

Category: Protein Protocols: Protein Phosphorylation Protocols

Paper describing methods for monitoring kinase activity, investigating kinaseâ€“substrate specificity, examining phosphorylation in planta and the determination of phosphorylation sites in a protein. In addition, strategic considerations for experimental design and variables will be discussed. Scott C. Peck, the Plant Journal. - [Read Analysis of protein phosphorylation: methods and strategies PDF]

Annealing, Cloning, and Sequencing of shRNA Linkers into pEN_H1 Plasmids Protocol - http://www.signaling-gateway.org/data/cgi-bin/ProtocolFile.cgi/afcs_PP00000230.pdf?pid=PP00000230

Category: RNAi Technology Protocols

Protocol describes the preparation of an shRNA-expressing Gateway entry vector. This process is preceded by the design and synthesis of target gene-specific sense and antisense oligonucleotides which, when annealed, will constitute an shRNA cassette. - [Read Annealing, Cloning, and Sequencing of shRNA Linkers into pEN_H1 Plasmids Protocol]

Antigen Design and Sera Purification - http://www.sigmaaldrich.com/Brands/Sigma_Genosys/Custom_Antisera/Key_Resources/Antigen_Design.html

Category: Immunology: Antigen

Antigen Design and Sera Purification. Custom antisera. Sigma Aldrich. Peptide Selection and Design, Coupling Strategy # Selecting the Protein Carrier, Multiple Antigenic Peptides (MAPs), Choice of Host, Adjuvant, Immunization, & Sera Collection, Antisera Purification, Ammonium Sulfate Precipitation, Protein A/G, Immunoaffinity Purification. - [Read Antigen Design and Sera Purification]

Basic Ideas in PCR Protocol Design. PDF - http://www.idtdna.com/support/technical/TechnicalBulletinPDF/A_Basic_PCR_Protocol.pdf

Category: DNA Protocols: PCR Polymerase Chain Reaction Protocols

Basic Ideas in PCR Protocol Design. PDF - [Read Basic Ideas in PCR Protocol Design. PDF]

Basic Ideas in PCR Protocol Design. PDF - http://www.idtdna.com/support/technical/TechnicalBulletinPDF/A_Basic_PCR_Protocol.pdf

Category: PCR Protocols

Basic Ideas in PCR Protocol Design. PDF - [Read Basic Ideas in PCR Protocol Design. PDF]

Calcium Phosphate Transfection Method - http://www.flemingtonlab.com/Protocols/CalciumPhosphateTransf.pdf

Category: Transfection Protocols: Calcium Phosphate Transfection Protocols

This calcium phosphate transfection method works best in cell lines that are 1) highly transformed and 2) adherent (Hela, U2OS, SAOS2, AdAH, NPC-KT and obtain from 20% to 100% transfection efficiency depending on the cell line). Works well for transient experiments but precautions should be used in the design and interpretation of experiments based on the discussion below. Also works very well for generating stable cell lines. This method is quite sensitive to the amount of input plasmid. - [Read Calcium Phosphate Transfection Method]

Cell Fractionation of a Mixed Population of Cells - http://www.axis-shield.com/densityhome/optiprep/C14.pdf

Category: Cell Biology and Cell Culture

Cell fractionation techniques are presented for the design of gradient systems for separating one or more cell types from lavages of body cavities or from mechanically or enzymically-dissociated tissues. Includes: Preparation of cell suspension for gradient loading; Fractionation by buoyant density; Fractionation on the basis of cell size. - [Read Cell Fractionation of a Mixed Population of Cells]

Cloning protocols/tips by Astrid PDF - http://www.its.caltech.edu/~bjorker/Protocols/cloning%20protocols%20by%20Astrid.pdf

Category: DNA Protocols: DNA Cloning

Cloning protocols/tips by Astrid. PCR and primer design, Extracting DNA from gel, Restriction of vector, Ligation, and Transformation. CalTech - [Read Cloning protocols/tips by Astrid PDF]

Design, Synthesis, and Characterization of Caged Compounds - http://www.cshprotocols.org/cgi/content/extract/2007/1/pdb.ip25

Category: Microscopy Protocols: Live-Cell Imaging Protocols

When choosing a particular molecule for photoactivation studies, it is necessary to have some structural knowledge of the molecule in order to design an appropriately caged species that will retain its biological inactivity until uncaging is effected. Includes synthesis of caged peptides or proteins. - [Read Design, Synthesis, and Characterization of Caged Compounds]

Design, Synthesis, and Characterization of Caged Compounds Protocol - http://www.cshprotocols.org/cgi/content/extract/2007/1/pdb.ip25

Category: Microinjection Protocols: Microinjection of Proteins Protocols

When choosing a particular molecule for photoactivation studies, it is necessary to have some structural knowledge of the molecule in order to design an appropriately caged species that will retain its biological inactivity until uncaging is effected. - [Read Design, Synthesis, and Characterization of Caged Compounds Protocol]

EMSA Protocol using 32-p. - http://www.well.ox.ac.uk/flint/EMSA.htm

Category: DNA Protocols: EMSA DNA-Protein Protocols

Primer design, Primer annealing, Primer labelling, Probe purification, In vitro hybridization DNA-protein Binding reaction. Jonathan Flint. - [Read EMSA Protocol using 32-p.]

Media for Culture of Mammalian Cells Protocol - https://catalog.invitrogen.com/index.cfm?fuseaction=iProtocol.unitSectionTree&treeNodeID=9E662B6F09C1BB8FBC47FC2A7E61A8A3&objectid=66739B890A55AC13354418E67F28E693

Category: Cell Biology and Cell Culture: Cell Culture Growth Media: Mammalian Cell Culture Growth Media Protocols

The culture medium is an essential component of the in vitro environment and must be selected or designed with care. This protocol provides guidelines for design of serum-containing and serum-free media, selective and specialty media, and media for growth under special conditions such as soft-agar growth. - [Read Media for Culture of Mammalian Cells Protocol]

Microarray Success - http://www.microarraysuccess.org

Category: DNA Microarray Protocols

The "7 keys to successful microarray analysis" has been designed to guide researchers step-by-step through the design, implementation, analysis, and publication of a microarray experiment. - [Read Microarray Success]

Mixed Oligonucleotide-primed Amplification of cDNA MOPAC Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/2/pdb.prot3484

Category: PCR Protocols: cDNA Synthesis Protocols

In MOPAC, the amino-terminal and carboxy-terminal sequences of a peptide are used to design two redundant families of oligonucleotides encoding the aminoand carboxy-terminal sequences of the peptide. The primers are used either to amplify a segment of cDNA prepared by RT-PCR from a tissue known to express the protein or to amplify a segment of DNA from an established genomic or cDNA library. - [Read Mixed Oligonucleotide-primed Amplification of cDNA MOPAC Protocol]

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 Program Design - http://info.med.yale.edu/genetics/ward/tavi/p08.html

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

The requirement of an optimal PCR reaction is to amplify a specific locus without any unspecific by-products. Therefore, annealing needs to take place at a sufficiently high temperature to allow only the perfect DNA-DNA matches to occur in the reaction. P - [Read PCR Program Design]

PCR Program Design - http://info.med.yale.edu/genetics/ward/tavi/p08.html

Category: PCR Protocols: PCR Optimization

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]

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]

SNP Cutter: SNP PCR-RFLP Assay Design - http://bioinfo.bsd.uchicago.edu/SNP_cutter.htm

Category: DNA Protocols: SNP Protocols

SNP Cutter: SNP PCR-RFLP Assay Design. By Ruifang Zhang, Zanhua Zhu, Fengxia Yao, Hongming Zhu, Tu Nguyen, Chunyu Liu - [Read SNP Cutter: SNP PCR-RFLP Assay Design]

SNP PCR Primer Design - http://www.changbioscience.com/primo/primosnp.html

Category: DNA Protocols: SNP Protocols

SNP PCR Primer Design. Chang Biosciences. - [Read SNP PCR Primer Design]

Transfection of IMEC Cells Using SuperFect Transfection Reagent Protocol - http://www.flemingtonlab.com/Protocols/SuperfectionofIMECcells.pdf

Category: Transfection Protocols

Transfection of IMEC cells using SuperFect Transfection Reagent protocol. Protocol includes experimental design considerations. - [Read Transfection of IMEC Cells Using SuperFect Transfection Reagent Protocol]

Transgenic - Universal Mouse Genotyping Protocol Using PCR - http://www.knockoutmousestation.com/mouse/detail/link-28.html

Category: Molecular Model Organisms: Mouse Animal Protocols: Mouse Genotyping Protocols

Description:, Universal Mouse Genotyping Protocol, Primer Design, PCR Cycling, HotSHOT Preparation of Murine DNA for PCR. WUSM. Mouse Genetics Core. ... - [Read Transgenic - Universal Mouse Genotyping Protocol Using PCR]

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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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