extraction Protocols

Category: Molecular Biology Protocols: Phage Protocols and Methods

Plating Lambda Phage to Generate Plaques. Elution of Phage. Phage DNA Extraction. Dr.Wurtzel. Dept. Biological Sciences, Lehman College. - [Read Phage Titer]

Category: RNA Protocols: rRNA Extraction and Isolation

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

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: Primary Cell Isolation and Culture Protocols: Laser Capture Microdissection Protocols

Protocol for the preparation of LCM of Paraffin embedded tissue sections. Includes: Fixation; Processing, Embedding and Tissue Sectioning; Staining; Laser Transfer; DNA Extraction Protocol of LCM tissue and PCR for DNA analysis; RNA Extraction Protocol of LCM tissue and RT-PCR for mRNA analysis. - [Read Preparation and LCM of Paraffin Embedded Tissue Sections Protocol]

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]

Category: Fungi Protocols

Protocol for the preparation of solid tissue for Aspergillus galactomannan antigen detection by Platelia (Biorad). Technique was designed for use on human serum. However, it may also be possible to perform this method on solid tissues and organic solutions. Viscous solution and tissue specimens need to be pre-treated to achieve the extraction of the Aspergillus antigen and to get a homogeneous sample in solution. - [Read Preparation of Solid Tissue for Aspergillus Galactomannan Antigen Detection by Platelia Protocol]

Category: Primary Cell Isolation and Culture Protocols: Laser Capture Microdissection Protocols

Protocol for the preparation, LCM and RNA/DNA extraction of frozen tissue sections. Includes: Embedding, Cutting and Staining. - [Read Preparation, LCM and RNA/DNA extraction of Frozen Tissue Sections Protocol]

Category: Molecular Biology Protocols: Phage Protocols and Methods: Lambda Phage Protocols

Detailed Lambda DNA Isolation and Extraction protocol with recipes. Stanford DNA Sequence & Technology Center. - [Read Preparing Lambda DNA]

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]

Category: Yeast Protocols: Yeast Protein Protocols: Yeast Protein Purification and Isolation Protocols

Protocol for protein extraction from Yeast. - [Read Protein Extraction from Yeast Protocol]

Category: Mass Spectrometry Protocols

Colloidal coomassie blue staining, Destaining, Reduction/Alkylation, Peptide extraction For MALDI-MS analysis and For MALDI-MS analysis protocols and methods. Institut Curie Paris. - [Read Proteomic protocols and Peptide Extraction]

Category: Protein Protocols: Protein Extraction Protocols

Protocol for Protein Extraction Using Proteomics. Extraction of proteins from plant cells that are rich in compounds that interfere with the 2-Dimensional electrophoretic separation methods such as salts, organic acids, phenolics, pigments, terpenes, among others. A common protocol used in our lab for extraction proteins from plant tissues consists in the homogenization of mortar-grounded material in liquid nitrogen with an extraction buffer. - [Read Protocol for Protein Extraction Using Proteomics]

Category: Primary Cell Isolation and Culture Protocols: Laser Capture Microdissection Protocols

Protocols for LCM preparation and analysis. Includes protocols: Preparation, LCM and RNA/DNA extraction of Frozen Tissue Sections; Preparation and LCM of Paraffin Embedded Tissue Sections; Standard Protocols for Microdissected Tissue Analysis. - [Read Protocols for LCM Preparation and Analysis]

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]

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]

Category: Yeast Protocols: Yeast Protein Protocols: Yeast Protein Purification and Isolation Protocols

Protocol for rapid and reliable preparation of total cell lysates from fission yeast. Method for successful and reproducible extraction of proteins from S. pombe cells. - [Read Rapid and Reliable Preparation of Total Cell Lysates from Fission Yeast Protocol]

Category: Cell Biology and Cell Culture: Cell Culture Techniques: Cell Line Preservation Freezing

Cell lines are reactivated and grown to a count of 1 x 108 cells. The cells are pelleted and stored frozen at -80 degrees C prior to DNA extraction. Donis-Keller. - [Read Reactivating Cell Lines and Cell Growth for DNA Preparation]

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]

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]

Category: Immunology

Removal of CCR5 ligands and induction of pro-resolving lipid mediators by apoptotic neutrophils during resolution. Application of lipid extraction from peritoneal exudates, in tandem with lipid mediator informatics can be used to determine the role of apoptotic neutrophils in the generation of resolution phase lipid mediators. This neutrophil transfer system allows the determination of the direct impact of apoptotic leukocytes in the resolution of inflammation. - [Read Removal of CCR5 Ligands and Induction of Pro-Resolving Lipid Mediators by Apoptotic Neutrophils]

Category: Nucleic Acid Purification Protocols: DNA Isolation Protocols

Ethidium bromide is removed from DNA by phase extraction with organic solvents. - [Read Removal of Ethidium Bromide from DNA by Extraction with Organic Solvents Protocol]

Category: RNA Protocols: RT-PCR and cDNA synthesis

RNA Extraction and cDNA from Pine Tree Needles - [Read RNA Extraction and cDNA from Pine Needles]

Category: Immunology: Immunoassays

Protocol for steroid radioimmunoassay. Includes: SOLVENT DISTILLATION; PREPARATION OF PLASMA SAMPLES; EXTRACTION OF STEROIDS AND COLUMN PACKING; COLUMN CHROMATOGRAPHY; RADIOIMMUNOASSAY; SEPARATION OF BOUND AND FREE COUNTS; DIRECT ASSAYS; SHORT COLUMN CHROMATOGRAPHY. - [Read Steroid Radioimmunoassay Protocol]

Category: Protein Protocols: Protein Extraction From Tissue

Tissue subcellular fractionation and protein extraction for use in mass-spectrometry-based proteomics. Although many methods exist for fractionating proteins, the method described here can capture the majority of subcellular fractions simultaneously at reasonable purity. The scalability of this method makes it amenable to small samples, such as embryonic tissues, in addition to larger tissues. The protocol described is for the general fractionation and extraction of proteins from organs / tissue - [Read Tissue subcellular fractionation and protein extraction for use in mass-spectrometry-based proteomic]

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]