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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]

Isolation of High-molecular-weight DNA from Mammalian Cells Using Proteinase K and Phenol Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/2/pdb.prot4036

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

Method of choice when large amounts of mammalian DNA are required, for example, for Southern blotting (Rapid Isolation of Mammalian DNA, Rapid Isolation of Yeast DNA, Southern Blotting: Capillary Transfer of DNA to Membranes) or for construction of genomic libraries in bacteriophage {lambda} vectors. Approximately 200 µg of mammalian DNA, 100-150 kb in length, is obtained from 5 x 107 cultured aneuploid mammalian cells (e.g., HeLa cells). - [Read Isolation of High-molecular-weight DNA from Mammalian Cells Using Proteinase K and Phenol Protocol]

Lowry Protein Assay - http://www.animal.ufl.edu/hansen/protocols/LOWRY.htm

Category: Protein Protocols: Lowry Protein Assay

Lowry Protein Assay. The Lowry procedure is one of the most venerable and widely-used protein assays, being first described in 1951 [Lowry et al., J. Biol. Chem. 193: 265-275 (1951)]. Under alkaline conditions, copper complexes with protein. When folin phenol reagent (phospho-molybdic-phosphotungstic reagent) is added, the Folin-phenol reagent binds to the protein. Bound reagent is slowly reduced and changes color from yellow to blue. P.J. Hansen, Dept. of Animal Sciences, University of Florida. - [Read Lowry Protein Assay]

Methods for DNA isolation - http://mycoplasmas.vm.iastate.edu/lab_site/methods/DNA/DNAisol.html

Category: DNA Protocols: DNA Extraction Protocols

Large scale double-stranded DNA isolation, Miniprep double-stranded DNA isolation, Large scale M13RF isolation, Single-stranded M13 DNA isolation using phenol. Minion Lab.Veterinary Medicine Iowa Univ. - [Read Methods for DNA 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]

Phenol Extraction of rRNA - http://homepages.gac.edu/~cellab/chpts/chpt14/ex14-7.html

Category: RNA Protocols: rRNA Extraction and Isolation

Phenol Extraction of rRNA from Rat Liver Tissue. Dr. William Heidcamp. - [Read Phenol Extraction of rRNA]

Phenol-based Protocol Isolation of DNA Fragments from Low-Melting Temperature Agarose - http://wheat.pw.usda.gov/~lazo/methods/101/101lmtagar.html

Category: DNA Protocols: DNA Extraction Protocols: Agarose Gel DNA Extraction Protocols

Phenol-based Protocol Isolation of DNA Fragments from Low-Melting Temperature Agarose. Reference: Favre, D. 1992. Biotechniques vol. 13. - [Read Phenol-based Protocol Isolation of DNA Fragments from Low-Melting Temperature Agarose]

Phenol/Freeze RNA Prep Protocol - http://www.fhcrc.org/science/labs/gottschling/yeast/rprep.html

Category: Yeast Protocols: Yeast Nucleic Acid Protocols: Yeast RNA Isolation Protocols

Protocol for phenol/freeze RNA prep. - [Read Phenol/Freeze RNA Prep Protocol]

Preparation of RNA from Paraffin-Embedded Fixed Tissue Using Trizol Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/1/pdb.prot4103

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

The method uses Trizol, a phenol-base reagent produced by Invitrogen. - [Read Preparation of RNA from Paraffin-Embedded Fixed Tissue Using Trizol Protocol]

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]

Preparation of Single-stranded Bacteriophage M13 DNA Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/2/pdb.prot3686

Category: Viral Manipulation Protocols: M13 Phage Manipulation Protocols

Bacteriophage M13 single-stranded DNA is prepared from virus particles secreted by infected cells into the surrounding medium. The filamentous particles are concentrated by precipitation from a high-ionic-strength buffer with polyethylene glycol. Subsequent extraction with phenol releases the single-stranded DNA, which is then collected by precipitation with ethanol. This protocol is generally used to prepare single-stranded DNA from a small number of M13 isolates. - [Read Preparation of Single-stranded Bacteriophage M13 DNA Protocol]

Protein extraction from whole tissues for isoelectric focusing - http://proteomics.missouri.edu/protocols/proteinExtraction.html

Category: Protein Protocols: Protein Extraction From Tissue

Protein extraction from whole tissues for isoelectric focusing. University of Missouri - Columbia Proteomics Center. SDS extraction followed by acetone precipitation. Also has Phenol extraction followed by methanolic ammonium acetate precipitation. - [Read Protein extraction from whole tissues for isoelectric focusing]

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 Animal Cells Using Trizol - http://www.cshprotocols.org/cgi/content/extract/2006/1/pdb.prot4104

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

Protocol for purification of RNA from animal cells using Trizol. Trizol is a phenol-based reagent produced by Invitrogen. - [Read Purification of RNA from Animal Cells Using Trizol]

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: Enzymatic Digestion with Agarase Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/2/pdb.prot4026

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

A fragment of gel containing a band of DNA is excised and digested with agarase, which hydrolyzes the polymer to disaccharide subunits. The released DNA is then purified by phenol extraction and ethanol precipitation. The method works well for DNAs ranging in size from <5 kb to >20 kb. - [Read Recovery of DNA from Low-melting-temperature Agarose Gels: Enzymatic Digestion with Agarase Protocol]

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]

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]

Articles (1-9 of 9)

Populational Analysis of Genomic DNA Protocol

A protocol on the populational Analysis of genomic DNA.

Lambda Phage Protocol for Large Preparation DNA Recovery

Lambda Phage Protocol for Large Preparations DNA Recovery.

Single Stranded Plasmid DNA Isolation Protocol

A Single Stranded Plasmid DNA Isolation Protocol describing the production and isolation of single-stranded DNA (ssDNA) using bacteriophagemid-containing bacteria and helper phage. Infection of the host cells with helper phage allows for packaging of ssDNA into bacteriophage. The ssDNA can then be isolated from phage particles.

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.

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.

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.

Histone H1 Kinase Activity Assay

Histone H1 Kinase Activity Assay Protocol. This protocol describes assaying kinase activity of a putative kinase using Histone H1 as the substrate. Histone H1 is the canonical kinase substrate in this type of assay. Phosphorylation of Histone H1 is assessed by SDS-Polyacrylamide gel electrophoresis followed by autoradiography.