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A Multiplex PCR Method to Define a Narrow Deleted Chromosomal Region of a Tumor Genome - http://www.cshprotocols.org/cgi/content/extract/2006/1/pdb.prot4117

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]

DNA Preparation from Blood PDF - http://www.riedlab.nci.nih.gov/publications/2438.2413_DNA_Prep_Blood.pdf

Category: DNA Protocols: DNA Extraction Blood

Method for DNA Preparation from Blood. Using lysis buffer and phenol/chloroform/isoamyl alcohol. Thomas Ried, NCI. - [Read DNA Preparation from Blood PDF]

Extraction of Bacteriophage lambda DNA from Large-scale Cultures Using Proteinase K and SDS Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/2/pdb.prot3972

Category: Viral Manipulation Protocols: Phage Lamda Manipulation Protocols

DNA is best isolated from bacteriophage lambda particles by digesting the viral coat proteins with a powerful protease such as proteinase K, followed by extraction with phenol:chloroform. This procedure is easily adapted for use with smaller-scale preparations of bacteriophage lambda. - [Read Extraction of Bacteriophage lambda DNA from Large-scale Cultures Using Proteinase K and SDS Protocol]

Extraction of Calf Brain Lipids Protocol - http://www.bio.com/protocolstools/protocol.jhtml?id=p1281

Category: Lipid Protocols

Protocol for the extraction of calf brain lipids. Protocol describes a rapid method to isolate lipids from bovine brain tissue using an organic solvent mixture of Chloroform and Methanol. - [Read Extraction of Calf Brain Lipids Protocol]

Extraction of the SecinH3 from Mouse Liver Protocol - http://www.natureprotocols.com/2006/12/15/extraction_of_the_secinh3_from.php

Category: Mouse Protocols

Mice fed with the cytohesin inhibitor SecinH3 for two days develop hepatic insulin resistance that can be identified by reduced liver glycogen levels, increased serum insulin and ketone body levels and decreased serum non-esterified fatty acid. To confirm the presence and identity of SecinH3 in mouse liver, we extracted the compound from liver homogenates with chloroform and identified it by LC/MS. - [Read Extraction of the SecinH3 from Mouse Liver Protocol]

Holzer's Stain Protocol - http://library.med.utah.edu/WebPath/HISTHTML/MANUALS/HOLZER.PDF

Category: Neuroscience Protocols: Neuronal Stains Protocols

An appropriate term for glial fibers is 'nerve glue', because they provide the internal support of the central nervous system. There are four types of glial cells: astrocytes, oligosendroglia,microglia, and ependymal cells. The glia fibers are stained with crystal violet which are resistant to the aniline-chloroform differentiating solution. - [Read Holzer's Stain Protocol]

Methanol-Chloroform Precipitation of Proteins - http://www.healthsystem.virginia.edu/internet/biomolec/methanolchloroform.cfm

Category: Mass Spectrometry Protocols

Methanol-Chloroform Precipitation of Proteins. A procedure for precipitating proteins from solution, including detergent solutions, is from Wessel and FlÃ¼gge (1984). Univ. Virginia. - [Read Methanol-Chloroform Precipitation of Proteins]

Methods for Plant RNA Isolation - http://wheat.pw.usda.gov/~lazo/methods/lazo/met6.html

Category: Plant Biology Protocols: Plant DNA RNA Isolation Protocols

AMES/Chloroform extraction to extract total RNA from potato leaves for viroid analysis. - [Read Methods for Plant RNA Isolation]

Phage Protocols - DNA Gels - http://www.rpgroup.caltech.edu/~paul/protocols/phage/lambda/gel/

Category: Molecular Biology Protocols: Phage Protocols and Methods

Phenol/chloroform DNA extraction, running a gel for DNA from Phages. Rob Phillips Group: Physical Biology of the Cell - [Read Phage Protocols - DNA Gels]

Preparation of RNA from Plant Tissue Using Guanidinium Isothiocyanate/Cesium Chloride Ultracentrifug - http://www.cshprotocols.org/cgi/content/extract/2006/1/pdb.prot4102

Category: Plant Biology Protocols: Plant DNA RNA Isolation Protocols

Tissues are homogenized in guanidinium isothiocyanate lysis buffer and then subjected to cesium chloride ultracentrifugation. The resulting RNA is then extracted with phenol and chloroform to remove protein and lipid contaminants. - [Read Preparation of RNA from Plant Tissue Using Guanidinium Isothiocyanate/Cesium Chloride Ultracentrifug]

Purification of Demethylated Sphingomyelin Protocol - http://www.duke.edu/web/ceramide/protocols/0032.html

Category: Lipid Protocols

Protocol for the purificiation of demethylated sphingomyelin. Includes: Lower, chloroform phase; Upper, aqueous phase and interphase. - [Read Purification of Demethylated Sphingomyelin Protocol]

Purification of Nucleic Acids by Extraction with Phenol:Chloroform Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/1/pdb.prot4455

Category: Nucleic Acid Purification Protocols

Protocol describes the standard method for nucleic acid purification by extraction first with phenol:chloroform (optionally containing hydroxyquiniline at 0.1%) and then with chloroform to remove any remaining phenol. The procedure takes advantage of the fact that deproteinization is more efficient when two different organic solvents are used instead of one. - [Read Purification of Nucleic Acids by Extraction with Phenol:Chloroform Protocol]

Purification of RNA from Cells and Tissues by Acid Phenol-Guanidinium Thiocyanate-Chloroform Extract - http://www.cshprotocols.org/cgi/content/extract/2006/2/pdb.prot4045

Category: Nucleic Acid Purification Protocols: RNA Isolation Protocols: RNA Isolation fromTissues or Cultured Cells Protocols

Single-step technique, cells are homogenized in guanidnium thiocyanate and the RNA is purified from the lysate by extraction with phenol:chloroform at reduced pH. Many samples can be processed simultaneously and speedily. The yield of total RNA depends on the tissue or cell source and is generally in the range of 4-7 µg/ml starting tissue or 5-10 µg/106 cells. IMPORTANT: Prepare all reagents used in this protocol with Diethyl pyrocarbonate (DEPC)-treated H2O. - [Read Purification of RNA from Cells and Tissues by Acid Phenol-Guanidinium Thiocyanate-Chloroform Extract]

Purification of RNA from Plant Tissue Using the Concert Plant Reagent - http://www.cshprotocols.org/cgi/content/extract/2006/1/pdb.prot4106

Category: Plant Biology Protocols: Plant DNA RNA Isolation Protocols

This protocol is not phenol-based, but does require the addition of chloroform. The Concert Plant Reagent is intended for the isolation of RNA from a wide variety of plant tissues including blue spruce needles, potato tuber etc. - [Read Purification of RNA from Plant Tissue Using the Concert Plant Reagent]

Recovery of DNA from Low-melting-temperature Agarose Gels: Organic Extraction Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/2/pdb.prot4025

Category: Nucleic Acid Electrophoresis Protocols: DNA Electrophoresis Protocols: DNA Electrophoresis in Agarose Gels Protocols

DNA fragments separated by electrophoresis through gels cast with low-melting-temperature agarose are recovered by melting the agarose and extracting the resulting solution with phenol:chloroform. The protocol works best for DNA fragments ranging in size from 0.5 kb to 5 kb. - [Read Recovery of DNA from Low-melting-temperature Agarose Gels: Organic Extraction Protocol]

Screening Expression Libraries Constructed in Plasmid Vectors Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/2/pdb.prot4079

Category: DNA Protocols: cDNA Library Protocols

A cDNA library constructed in a plasmid expression vector of the pUC, pUR, or pEX series is plated on agar medium and then replicated onto filters, which are transferred to plates containing IPTG. After 2-4 hours of induction, the colonies are lysed with chloroform and then screened with appropriate antibodies. - [Read Screening Expression Libraries Constructed in Plasmid Vectors Protocol]

Simple Mini-prep Protocol - http://irc.igd.cornell.edu/Protocols/Mini-prep.htm

Category: Microbiology: Mini-Prep Plasmid Purification

Simple Mini-prep Protocol, using Chloroform/Isoamyl alcohol (IAA). Cornell. - [Read Simple Mini-prep Protocol]

Total RNA isolation (Guanidinium Thiocyanate-Phenol-Chloroform Extraction) Protocol - http://www.flemingtonlab.com/Protocols/TotalRNAprep.pdf

Category: Nucleic Acid Purification Protocols: RNA Isolation Protocols

Protocol for total RNA isolation. This method is fast and works well for preparation of total RNA. We typically use total RNA for quantitative S1 nuclease analysis of endogenous (or in vitro) gene expression, and this method works well for this purpose. - [Read Total RNA isolation (Guanidinium Thiocyanate-Phenol-Chloroform Extraction) Protocol]

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Lambda Phage Protocol for Large Preparation DNA Recovery

Lambda Phage Protocol for Large Preparations DNA Recovery.

Lambda Phage Protocol Large DNA Preparation

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.

Acid Guanidinium Thiocyanate RNA Isolation Phenol Chloroform Extraction

A single step RNA isolation protocol using Phenol Chloroform Extraction and Acid Guanidinium Thiocyanate. This RNA isolation method uses the fact that guanidinium thiocyanate can simultaneously lyse the cells and inactive cellular RNAses during the initial RNA isolation step allow a single step in the method.

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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