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AFLP protocol - http://www.msu.edu/user/hazensam/aflp/AFLPprotocolMSU.html

Restriction Digestion of Genomic DNA , Adapter preparation, Ligation of Adapters. Pre amplification Reactions. Gel electrophoresis, Silver Staining. AFLP Protocol and procedure. - [Read AFLP protocol]

AFLP protocol Wolf Lab - http://bioweb.usu.edu/wolf/aflp_protocol.htm

Category: PCR Protocols: AFLP PCR

Restriction and Ligation reactions, Setting up the reactions, AFLP PCR reactions protocols. Analyzing the data using Genescan. Paul G. Wolf, Utah State Univ. - [Read AFLP protocol Wolf Lab]

Antibody Addition and Detection for Staining Caenorhabditis elegans Protocol - http://www.cshprotocols.org/cgi/content/abstract/2006/23/pdb.prot4523

Category: C. elegans Protocols: C. elegans Staining Protocols

Extreme care should be used to identify and verify positive reactions, however, because cross-reactions are common. Counterstaining is essential for examining worms by immunofluorescence and is used to identify the exact cell in which an antigen appears. Methods for counterstaining include labeling all cells with a fluorescent dye that is specific for nucleic acids (e.g., DAPI or propidium iodide) and using GFP driven by tissue-specific promoters. - [Read Antibody Addition and Detection for Staining Caenorhabditis elegans Protocol]

Basic Information on In Vitro Transcription - http://www.ambion.com/techlib/basics/transcription/index.html

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]

Counterstains Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/1/pdb.prot4338

Category: Cell Culture Protocols: Cell Staining Protocols

Counterstains are used to help differentiate the various cell types of subcellular structures seen in cell staining. They are essential for tissue sections, allowing the identification of the cell types, but also may be helpful in other staining reactions. - [Read Counterstains Protocol]

Cycle Sequence Reactions For Large Insert Plasmid Templates Protocol - http://bacpac.chori.org/cyclesere.htm

Category: DNA Protocols: DNA Sequencing Protocols

Protocol for cycle sequence reactions for large insert plasmid templates. Includes: CycleSequenceConditions; Primers Useful For BAC and PAC Vectors. - [Read Cycle Sequence Reactions For Large Insert Plasmid Templates Protocol]

Dealing with Carryover Contamination in PCR: An Enzymatic Strategy Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/1/pdb.prot4092

Category: PCR Protocols

Protocol for dealing with carryover contamination in PCR- enzymatic strategy. Repeated use of PCR and manipulation of its products cause aerosols that can contaminate neighboring samples and work areas. Such "carryover contamination" can be prevented by including dUTP in place of dTTP for all amplification reactions. - [Read Dealing with Carryover Contamination in PCR: An Enzymatic Strategy Protocol]

Dideoxy-mediated Sequencing of DNA Using Taq DNA Polymerase Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/2/pdb.prot3803

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

Because sequencing reactions catalyzed by thermostable DNA polymerasessuch as Taq are carried out at elevated temperatures, problemscaused by mismatched annealing of primers or templates richin secondary structure are greatly alleviated. - [Read Dideoxy-mediated Sequencing of DNA Using Taq DNA Polymerase Protocol]

Dideoxy-mediated Sequencing Reactions Using Bacteriophage T7 DNA Polymerase (Sequenase) Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/2/pdb.prot3801

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

Protocol describes DNA-sequencing of single-stranded DNAtemplates in reactions catalyzed by Sequenase. - [Read Dideoxy-mediated Sequencing Reactions Using Bacteriophage T7 DNA Polymerase (Sequenase) Protocol]

Dideoxy-mediated Sequencing Reactions Using PCR and End-labeled Primers Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/2/pdb.prot3791

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

In this protocol asymmetric PCR is used to generate single-strandedDNA templates for dideoxy-sequencing - [Read Dideoxy-mediated Sequencing Reactions Using PCR and End-labeled Primers Protocol]

Dideoxy-mediated Sequencing Reactions Using the Klenow Fragment of E. coli DNA Polymerase - http://www.cshprotocols.org/cgi/content/extract/2006/2/pdb.prot3802

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

Protocol for dideoxy-mediated sequencing reactions using the Klenow fragment of E. coli DNA polymerase I and single-stranded DNA templates. - [Read Dideoxy-mediated Sequencing Reactions Using the Klenow Fragment of E. coli DNA Polymerase]

Dideoxy-mediated Sequencing Reactions Using the Klenow Fragment of E. coli DNA Polymerase I - http://www.cshprotocols.org/cgi/content/extract/2006/2/pdb.prot3802

Category: E Coli Protocols: E coli Nucleic Acid Protocols

Protocol for dideoxy-mediated sequencing reactions using the Klenow Fragment of E. coli DNA polymerase I and single-stranded DNA templates. - [Read Dideoxy-mediated Sequencing Reactions Using the Klenow Fragment of E. coli DNA Polymerase I]

DNA Sequencing Methods - http://www.genome.ou.edu/protocol_book/protocol_partIV.html#IV.C

Category: DNA Protocols: DNA Sequencing Protocols

Methods for DNA sequencing. Includes: Bst-catalyzed radiolabeled DNA sequencing; Radiolabeled sequencing gel preparation, loading, and electrophoresis; Taq-polymerase catalyzed cycle sequencing using fluorescent-labeled dye primers; Taq-polymerase catalyzed cycle sequencing using fluorescent-labeled dye terminator reactions; Sequenase[TM] catalyzed sequencing with dye-labeled terminators; etc. - [Read DNA Sequencing Methods]

Dye Protocols and Notes for Cosmid, BAC, BAC, Fosmid Templates - http://www.genome.ou.edu/big_dyes_cos_bac_pac_fos.html

Category: BACs Bacterial Artificial Chromosome Protocols

Sequencing conditions tested for the ABI Big-Dye terminators (PE-ABI #4303150 for the 1000 reaction kit - Description: TF,KIT BTD RR-1000) with various templates. Important to quantitate all templates by agarose gel electrophoresis vs size and concentration standards and do a few tests with different template concentrations to determine the optimal conditions for your reactions. Several conditions are given. - [Read Dye Protocols and Notes for Cosmid, BAC, BAC, Fosmid Templates]

Dye Terminator Cleanup for Automated DNA Sequencing Reactions Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/1/pdb.prot4101

Category: DNA Protocols: DNA Sequencing Protocols

Protocol describes a simple procedure for purifying sequencing reactions using the MagneSil particles from Promega. - [Read Dye Terminator Cleanup for Automated DNA Sequencing Reactions Protocol]

In Vitro Splicing Reactions in Drosophila KC or HeLa Nuclear Extracts - http://www.bio.com/protocolstools/protocol.jhtml%3Bjsessionid%3D34E3CBZRBQMFZR3FQLMCFEWHUWBNSIV0?id=p519

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

Protocol for in vitro splicing reactions in Drosophila KC or HeLa nuclear extracts. Protocol includes: Procedure, Solutions, BioReagents and Chemicals and protocol hints. - [Read In Vitro Splicing Reactions in Drosophila KC or HeLa Nuclear Extracts]

In Vitro Transcription and Translation Using the Coupled Reticulocyte Lysate System - http://www.bio.com/protocolstools/protocol.jhtml?id=p594

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

Protocol for in vitro transcription and translation using the coupled reticulocyte lysate system. This protocol is designed to test random samples on a protein gel. Scale up the reactions accordingly. Protocol includes: Procedure, Solutions, BioReagents and Chemicals and protocol hints. - [Read In Vitro Transcription and Translation Using the Coupled Reticulocyte Lysate System]

In Vitro Transcription Protocol - http://www.cvmbs.colostate.edu/mip/wiluszlab/protocols/invitrotrans.htm

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

Protocol for in vitro transcription. Includes information on: Hot transcription reactions, notes and troubleshooting. - [Read In Vitro Transcription Protocol]

Kinase Assay Using In Vitro Translated Xenopus Mos Kinase - http://www.bio.com/protocolstools/protocol.jhtml?id=p912

Category: Signalling Signal Transduction Protocols

Protocol describes how tagged Mos kinase is translated in vitro, immunopurified, and used in a kinase assay. Protocol includes: Translation of Xenopus Mos Kinase; Antibody to Antigen Binding; Protein A Sepharose to Antibody Binding; Kinase Reactions on Immunoprecipitated Material; Polyacrylamide Gel Analysis of Immunoprecipitates. Includes protocol hints. - [Read Kinase Assay Using In Vitro Translated Xenopus Mos Kinase]

Ligation of Bacteriophage lambda Arms to Fragments of Foreign Genomic DNA Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/2/pdb.prot3980

Category: Viral Manipulation Protocols: Phage Lamda Manipulation Protocols

Pilot ligations and packaging reactions are used to establish the amounts of fragmented genomic DNA and bacteriophage {lambda} arms that yield the maximum number of recombinants. Additional ligation and packaging reactions may then be set up to yield a comprehensive library of genomic DNA. - [Read Ligation of Bacteriophage lambda Arms to Fragments of Foreign Genomic DNA Protocol]

Multiplex Real-Time PCR Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/1/pdb.prot4113

Category: PCR Protocols: Real-Time PCR Protocols

In multiplex real-time PCR, different sets of primers with different labels are used to amplify separate genes from the template DNA in one tube. This protocol uses LUX (Light Upon eXtension) primers from invitrogen. FAM (6-carboxy-fluorescein) is used to label the gene of interest, and JOE (6-carboxy-4', 5'-dichloro-2',7'-dimethoxy-fluorescein) is used to label a housekeeping gene as an internal control to normalize between different reactions. - [Read Multiplex Real-Time PCR Protocol]

Partial Digestion of Eukaryotic DNA for Use in Genomic Libraries: Pilot Reactions Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/2/pdb.prot3978

Category: Nucleic Acid Purification Protocols: DNA Isolation Protocols: Genomic DNA Isolation Protocols

Protocol is used to establish conditions for restriction enzyme digestion of eukaryotic genomic DNA that will generate fragments of a size appropriate for construction of genomic libraries. To construct a genomic library, the average length of the starting genomic DNA should be at least eight times the capacity of the vector. - [Read Partial Digestion of Eukaryotic DNA for Use in Genomic Libraries: Pilot Reactions Protocol]

Partial Digestion of Eukaryotic DNA for Use in Genomic Libraries: Preparative Reactions Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/2/pdb.prot3979

Category: Nucleic Acid Purification Protocols: DNA Isolation Protocols: Genomic DNA Isolation Protocols

The results of the pilot experiment (Partial Digestion of Eukaryotic DNA for Use in Genomic Libraries: Pilot Reactions) are used to establish conditions for partial digestion of eukaryotic DNA in the large-scale reactions described here. - [Read Partial Digestion of Eukaryotic DNA for Use in Genomic Libraries: Preparative Reactions Protocol]

Photosynthesis and Respiration - Introduction - http://homepages.gac.edu/~cellab/chpts/chpt8/intro8.html

Category: Plant Biology Protocols: Photosynthesis and Respiration Protocols

The physiological reactions of mitochondria and chloroplasts can be reduced to a series of electron transfers, catalyzed by specific enzymes found within the organelles. Thus, we can study the component processes of photosynthesis and respiration by isolating the organelles and measuring specific enzyme activity associated with that organelle. - [Read Photosynthesis and Respiration - Introduction]

Preparation of Myocyte RNA for Microarray Analysis Protocol - http://www.signaling-gateway.org/data/cgi-bin/ProtocolFile.cgi/afcs_PP00000133.pdf?pid=PP00000133

Category: Microarray Protocols: Microarray Analysis Protocols

Protocol permits the isolation of at least 3 µg of total RNA from approximately 150,000 cultured cardiac myocytes from adult mice. Includes: Treatment of Samples and Termination of Reactions; Isolation of RNA; Use of Environmental Chamber. - [Read Preparation of Myocyte RNA for Microarray Analysis Protocol]

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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.

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