genome Protocols

Category: Plant Biology Protocols: Plant Genetics Protocols

Microsatellite markers, also referred to as STMS (SequenceTagged Microsatellite Sites) or STR (Short Tandem Repeats) are widely used as molecular markers for intraspecific genotyping, molecular mapping and breeding purposes. The method described is an efficient,fast and relatively inexpensive way to obtain microsatellite markers without post-cloning selection methods. So far, the method has been successful in onion (Allium cepa L.), a plant with a large genome and for pathogenic fungi. - [Read Enrichment for Microsatellite Sequences in Onion (Allium cepa L.) Protocol]

Category: Chromatography Protocols: Column Chromatography Protocols

Fragment purification on Sephacryl S-500 spin columns , Bruce A. Roe. - [Read Fragment purification on Sephacryl S-500 spin columns]

Category: Plant Biology Protocols: Arabidopsis Genetics Protocols

Protocol for genetic mapping of Arabidopsis centromeres using PCR-based markers. Includes: DNA markers facilitate genome analysis; Centromere mapping using tetrad analysis; Preparation of DNA from frozen plant tissue. - [Read Genetic Mapping of Arabidopsis Centromeres Using PCR-Based Markers Protocol]

Category: Yeast Protocols: Yeast Protein Protocols: Yeast Protein Protein Interactions Protocols

This procedure capitalizes on the asexual/sexual reproductive cycle of yeast cells. Laboratory yeast strains can be maintained indefinitely by asexual reproduction as one of two haploid mating types, MATa or MAT{alpha}. - [Read Genome-Wide Analysis of Protein-Protein Interactions Using a Two-Hybrid Array]

Category: Yeast Protocols: Yeast Protein Protocols: Yeast Protein Protein Interactions Protocols

This protocol describes how to handle arrayed yeast using robotics. - [Read Genome-Wide Analysis of Protein-Protein Interactions Using a Two-Hybrid Array:]

Category: Yeast Protocols: Yeast Protein Protocols: Yeast Protein Protein Interactions Protocols

This protocol describes the first step in constructing an array: amplification of the predicted ORFs that are to be included in the array. Gene-specific primers containing vector-specific flanking sequences that facilitate recombinational cloning are used to amplify each ORF. A secondary amplification can be used to extend the length of the homologous vector sequence flanking the ORF. - [Read Genome-Wide Analysis of Protein-Protein Interactions Using a Two-Hybrid Array: Amplification of ORFs]

Category: Yeast Protocols: Yeast Protein Protocols: Yeast Protein Protein Interactions Protocols

This protocol describes three different storage methods for the array. Frozen stocks are the most permanent method and are an absolute requirement for maintaining a record of the array. - [Read Genome-Wide Analysis of Protein-Protein Interactions Using a Two-Hybrid Array: S]

Category: Microarray Protocols: Microarray Analysis Protocols

Genome-wide analysis of data generated on the Affymetrix 10K Xba 142 arrays for identification of regions with high probability to contain genes responsible for Micronodular (non-pigmented) Adrenocortical Hyperplasia. - [Read Genome-Wide Analysis Protocol]

Category: Yeast Protocols: Yeast Genetics Protocols

Protocol for genome-wide expression. - [Read Genome-Wide Expression Protocol]

Category: DNA Protocols: DNA Extraction Blood

Genomic DNA isolation from blood. Roe Lab - [Read Genomic DNA isolation from blood]

Category: Nucleic Acid Modification Protocols: Nucleic Acid Labeling Protocols

Protocol for genomic DNA labeling. - [Read Genomic DNA Labeling Protocol]

Category: DNA Protocols: DNA Sequencing Protocols: LICOR Sequencing Protocols

Protocol for LICOR terminator sequencing. - [Read LICOR Terminator Sequencing Protocol]

Category: DNA Protocols: DNA Extraction Protocols

Large scale double-stranded DNA isolation, Midiprep double-stranded DNA isolation. Bruce A. Roe, Department of Chemistry and Biochemistry, The University of Oklahoma, Norman. - [Read Methods for DNA isolation - Protocol Book]

Category: Cytogenetics Protocols

Protocol describes a recently developed method — methylation-specific digital karyotyping (MSDK) — that enables comprehensive and unbiased genome-wide DNA methylation analysis. Using a combination of a methylation-sensitive mapping enzyme (for example, AscI) and a fragmenting enzyme (for example, NlaIII), short sequence tags can be obtained and uniquely mapped to genome location. - [Read Methylation-Specific Digital Karyotyping Protocol]

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]

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

PCR Tips and Tricks - General Guidelines and Troubleshooting PCR polymerase chain reaction. The Genomic Variation Laboratory, U.C Davis - [Read PCR Tips and Tricks]

Category: PCR Protocols: PCR Optimization

PCR Tips and Tricks - General Guidelines and Troubleshooting PCR polymerase chain reaction. The Genomic Variation Laboratory, U.C Davis - [Read PCR Tips and Tricks]

Category: Plant Biology Protocols: Plant DNA RNA Isolation Protocols

A. thaliana has a very small haploid genome and this makes obtaining DNA somewhat difficult. The most notable problem is that DNA is usually contaminated with polysaccharide which inhibit restriction enzymes as well as other DNA modifying enzymes. This problem is most easily solved by using young plants which have not accumulated as much polysaccharide as older plants. The best results are obtained with plants that are two to three weeks post germinated. - [Read Plant DNA Extraction Protocol]

Category: DNA Protocols: DNA Sequencing Protocols: Big Dye Protocols

Protocol for plasmid templates for Big Dye. - [Read Plasmid Templates for Big Dye Protocol]

Category: DNA Protocols: DNA Cloning

Protocols for Recombinant DNA Isolation, Cloning, and Sequencing. Roe and Crabtree. - [Read Protocols for Recombinant DNA Isolation, Cloning, and Sequencing.]

Category: Nucleic Acid Detection Protocols

Restriction landmark genomic scanning (RLGS) is a method to detect large numbers of restriction landmarks in a single experiment.  It is based on the concept that restriction enzyme sites can serve as landmarks throughout a genome.  RLGS uses direct end-labeling of the genomic DNA digested with a rare-cutting restriction enzyme and high-resolution two-dimensional electrophoresis. - [Read Restriction Landmark Genomic Scanning Protocol]

Category: DNA Protocols: DNA Sequencing Protocols

Protocol for sequencing difficult regions on DNA. - [Read Sequencing Difficult DNA Regions Protocol]

Category: DNA Protocols: PCR Polymerase Chain Reaction Protocols

Single tube confirmation PCR protocol. Saccharomyces Genome Deletion Project. - [Read Single tube confirmation PCR protocol]

Category: PCR Protocols

Single tube confirmation PCR protocol. Saccharomyces Genome Deletion Project. - [Read Single tube confirmation PCR protocol]

Category: Microarray Protocols: Microarray Hybridization Protocols

Protocol for spotted microarray hybridization and scan. Includes: Setup Hybridization; Wash Slides; Scan Slides. - [Read Spotted Microarray Hybridization and Scan Protocol]