chromosomal Protocols

Category: Genetics and Genomics: Cancer Genetics Protocols: Loss of Heterozygosity Protocols

DNA for analysis is purified using salt precipitation. The method is gentle, limits the breakage of the long chromosomal strands, and avoids the use of phenol and chloroform. It is suitable for use with cultured cells, breast tumor tissue that has been subjected to hormone receptor analysis, and blood samples. The loss of heterozygosity assay is performed using a multiplex PCR, in which one of each primer pair is labeled with a different fluorophor. - [Read A Multiplex PCR Method to Define a Narrow Deleted Chromosomal Region of a Tumor Genome]

Category: BACs Bacterial Artificial Chromosome Protocols

Describe a set of BACs that map close to the centromeric and distal chromosomal ends for each mouse chromosome. - [Read A Triple Color FISH Technique for Mouse Chromosome Identification]

Category: Cytogenetics Protocols: Spectral Karyotyping SKY Protocols

SKY has been applied to various tumor groups including hematological malignancies, sarcomas, carcinomas and brain tumors, with the intent of identifying specific chromosomal abnormalities that may provide insight to the genes involved in the disease process as well as identifying recurrent cytogenetic markers for clinical diagnosis and prognostic assessment. - [Read Applications of SKY in Cancer Cytogenetics]

Category: Reporter Gene Assays: B-Galactosidase Assay Protocols

This assay is used when working with phage vectors carrying the beta-gal gene. If the cloning event disrupts a normally functional copy of the gene in the vector the resulting plaques would appear clear in the assay. If the phages contain a functional beta-gal gene they will form blue rings around their plaques. Any strain which is not an overproducer of beta-gal will work as indicator host bacteria; a single chromosomal copy of the gene is not a problem. - [Read Assay for Phage Containing the Beta-galactosidase Gene]

Category: Nucleic Acid Purification Protocols: DNA Isolation Protocols: DNA Isolation from Mammalian Cells Protocols

Protocol for chromosomal DNA preparation. Protocol was developed for cultured cells but should be appropriate for dissociated tissues as well. - [Read Chromosomal DNA Preparation Protocol]

Category: Cytogenetics Protocols

CGH provides a comprehensive picture of all chromosomal gains and losses within a single experiment. In contrast to banding analysis, CGH requires no preparation of metaphase chromosomes from the cells to be analyzed (which in certain tumor types may be difficult or even impossible). - [Read Detection of Chromosomal Imbalances Using DOP-PCR and Comparative Genomic Hybridization (CGH)]

Category: Cytogenetics Protocols: Spectral Karyotyping SKY Protocols

Protocol for the Detection of chromosomal imbalances using DOP-PCR and comparative genomic hybridization (CGH). Includes: Preparation and labeling of DOP-PCR products; Comparative genomic hybridization (CGH). - [Read Detection of Chromosomal Imbalances using DOP-PCR and Comparative Genomic Hybridization (CGH)]

Category: DNA Protocols: DNA Extraction Protocols

Allows students to easily isolate chromosomal DNA from onion cells using the same basic tools and methods that scientists use in the lab. A good introduction to using pipettes. Kate Dollard - [Read DNA Isolation from Onion Cells]

Category: Cytogenetics Protocols: Fluorescent In Situ Hybridization FISH Protocol

Protocol for fluorescence in situ hybridization (FISH) for DNA replication origins. Fluorescent in situ hybridization (FISH) is a molecular cytogenetic technique used for the detection of specific chromosomal rearrangements and applicable to many different specimen types. FISH is widely used for several diagnostic applications. - [Read Fluorescence In Situ Hybridization (FISH) for DNA Replication Origins Protocol]

Category: DNA Protocols: SNP Protocols

High-resolution SNP mapping by denaturing HPLC. A SNP mapping procedure that relies on resolving polymorphisms by denaturing HPLC without the necessity of determining the nature of the SNPs. They demonstrate the use of denaturing high-performance liquid chromatography to identify mutations in the candidate genes and to fine-map chromosomal breakpoints. - [Read High-resolution SNP mapping by denaturing HPLC]

Category: Fungi Protocols: Neurospora Protocols

Protocol guide for the N. crassa yeast artificial chromosome library. Includes: Chromosome Walking; Hybridization screening of the YAC library; YAC restriction mapping and contig building; Preparation of chromosomal DNA plugs of YAC clones; Partial restriction enzyme digestion of YAC DNA plugs; Using CHEF gel analysis to resolve YAC clones; Southern Hybridization; Isolation of terminal restriction fragments from cloned DNA inserts in YAC clones; etc. - [Read Protocol Guide for the N. crassa Yeast Artificial Chromosome Library]

Category: Yeast Protocols: Yeast Genetics Protocols: YACs Protocols

Protocol for sizing of YAC clones. To determine the size of a yeast artificial chromosome within the background of the normal yeast chromosomal complement. - [Read Sizing of YAC Clones Protocol]

Category: Yeast Protocols: Yeast Nucleic Acid Protocols: Yeast DNA Isolation Protocols

Protocol for Yeast chromosomal DNA prep. - [Read Yeast Chromosomal DNA Prep Protocol]