required Protocols

Category: Microscopy Protocols: Live-Cell Imaging Protocols

Protocol on the details required of support slide construction for a sealed preparation for long-term observations of cultured cells. - [Read A Sealed Preparation for Long-Term Observations of Cultured Cells: Support Slide Construction]

Category: Protein Protocols: Protein Quantitation Concentration Protocols

Absorbance assays are fast and convenient, since no additional reagents or incubations are required.  No protein standard need be prepared.  The assay does not consume the protein.  The relationship of absorbance to protein concentration is linear.  Because different proteins and nucleic acids have widely varying absorption characteristics there may be considerable error, especially for unknowns or protein mixtures. - [Read Absorbance Assay 280 nm]

Category: Cell Biology and Cell Culture: Apoptosis Protocols: Apoptosis Analysis

Analysis of DNA Fragmentation Using Agarose Gel Electrophoresis Shailaja Kasibhatla et al. This protocol provides a qualitative method for assessing cell death by detecting DNA fragments using agarose gel electrophoresis. One of the classic features of apoptosis is the cleavage of the genomic DNA into oligonucleosomal fragments represented by multiples of 180-200 bp. Visualizing these fragments can aid in characterizing an apoptotic event. May be combined with more quantitative methods. - [Read Analysis of DNA Fragmentation Using Agarose Gel Electrophoresis (Subscription Required)]

Category: Cell Biology and Cell Culture: Apoptosis Protocols: Apoptosis Analysis

Analysis of DNA Fragmentation Using the JAM Assay. By Shailaja Kasibhatla et al., The JAM assay is based on labeling nuclear DNA of cycling cells with [3H]thymidine and harvesting samples on glass fiber filters. Apoptosis will generate DNA fragments small enough to pass through the glass fiber filter, resulting in decreased radioactivity of the particular sample. Cell-mediated cytotoxicity or cell killing mediated by cytotoxic T lymphocytes (CTL) can also be measured by this technique. - [Read Analysis Of DNA Fragmentation Using The JAM Assay (Subscription Required)]

Category: Cell Culture Protocols: Sterile Technique Protocols

Cultured mammalian cells are used extensively in cell biology studies; it requires a number of special skills in order to be able to preserve the structure, function, behavior and biology of the cells. This unit describes the basic skills required to maintain and preserve cell cultures: aseptic technique, medium characteristics, passaging, freezing and storage, recovering frozen stocks, and counting viable cells. - [Read Basic Techniques for Mammalian Cell Tissue Culture Protocol]

Category: Primary Cell Isolation and Culture Protocols: Mammalian Cell Culture Protocols

Cultured mammalian cells are used extensively in cell biology studies; it requires a number of special skills in order to be able to preserve the structure, function, behavior and biology of the cells. This unit describes the basic skills required to maintain and preserve cell cultures: aseptic technique, medium characteristics, passaging, freezing and storage, recovering frozen stocks, and counting viable cells. - [Read Basic Techniques for Mammalian Cell Tissue Culture Protocol]

Category: Cell Biology and Cell Culture: Apoptosis Protocols: Apoptosis Analysis

Biochemical Analysis Of Cell Death Using Colorimetric Quantification Of Caspase Activation (Subscription Required). Biochemical Analysis of Cell Death Using Colorimetric Quantification of Caspase Activation Shailaja Kasibhatla et al., - [Read Biochemical Analysis Of Cell Death Using Colorimetric Quantification Of Caspase Activation (Subscrip]

Category: Cytogenetics Protocols: DIG Biotin Labeled Probe Protocols

This protocol describes how to use DIG Chem-Link to directly label any DNA [e.g. plasmids, PCR products, cDNA prepared from mRNA] or RNA (e.g. total RNA, poly(A)+ mMRNA). The DIG Chem-Link or Biotin Chem-Link may also be used to label oligonucleotides. Includes: Required Purity of DIG Chem-Link Templates; Direct DIG Labeling of mRNA or cDNA with DIG Chem-Link; Key Product Required for Direct Labeling of DNA or RNA; Estimating the Yield of DIG-labeled Nucleic Acids. - [Read Chem-Link Labeling of DNA or RNA with DIG or Biotin Protocol]

Category: Chromatography Protocols: Liquid Chromatography Protocols

Protocol for configuration, column construction, and column packing for a capillary liquid chromatography system. Protocol describes a procedure for adapting conventional HPLC systems to provide accurate low-flow rates (0.4-4 µl/min) and gradients required to operate slurry-packed capillary columns.  A key component of this system is a commercial axial-beam longitudinal flow cell that can be fitted to several commercial UV detectors. - [Read Configuration Column Construction Column Packing for Capillary Liquid Chromatography]

Category: DNA Protocols: Genomic DNA Library Protocols

This stage summarizes how to construct a cDNA library in a mammalian vector, using commercial kits. These kits are available from several manufacturers and generally include all the required reagents. - [Read Construction of cDNA Libraries in Eukaryotic Expression Vectors for Construction and Screening]

Category: Stem Cell Protocols

This protocol decribes derivation of TS cell lines from 3.5-days post coitum (dpc) mouse blastocysts. The procedure is similar to the derivation of embryonic stem (ES) cell lines. However, the success rate is considerably higher, and less expertise is required to recognize pluripotent TS cell colonies. - [Read Derivation of Trophoblast Stem (TS) Cell Lines from Blastocysts Protocol]

Category: Cell Biology and Cell Culture: Apoptosis Protocols: Apoptosis Analysis

Detection of Phosphatidylserine Externalization During Apoptosis. Shailaja Kasibhatla et al. An early event in apoptosis is the externalization of phosphatidylserine (PS), a phospholipid normally restricted to the inner leaflet of the plasma membrane. This apoptotic event can be monitored using Annexin V, a PS-specific binding protein. This protocol uses Annexin V-FITC as a probe, but Annexin V-biotin is also available, and binding can be revealed using streptavidin-FITC or oth - [Read Detection Of Phosphatidylserine Externalization During Apoptosis (Subscription Required)]

Category: Chromatography Protocols: DNA RNA Affinity Chromatography

DNA Affinity Chromatography, DNA affinity chromatography can be a low-tech method using gravity flow at 4°C, a disposable chromatography column, and DNA affinity resin prepared in the laboratory (see Preparation of a DNA Affinity Column). Include 10-20% glycerol and 0.025-0.1% NP-40 in the column buffers to suppress losses due to nonspecific adsorption of protein to surfaces. Load the protein in a buffer that is compatible with binding of the protein to its target site. Keith Brocklehurst et al - [Read DNA Affinity Chromatography Using Gravity Flow - Subscription Required]

Category: Molecular Biology Protocols: DNA Ligation Protocols

Description and protocol of the steps required to join together plasmid and insert fragments to create a new plasmid. Paul Kaufman, Univ California. - [Read DNA Ligation]

Category: Plant Biology Protocols: Arabidopsis Genetics Protocols

EMS is used at concentrations that induce multiple point mutations in each plant, such that mutant alleles of a specific locus are found at a rate of ~1 in 2000-5000 M2 plants. This high rate of mutagenesis makes possible the screening of relatively few plants to find those with the phenotype of interest, a particular advantage if the screen is laborious or if only a small number of genes mutate to the required phenotype. - [Read EMS Mutagenesis of Arabidopsis Seed Protocol]

Category: DNA Microarray Protocols

This protocol describes the steps required to produce a cDNA microarray. Gene-specific DNA is produced by PCR amplification of purified template plasmid DNAs from cloned ESTs. The PCR product is purified by ethanol precipitation, thoroughly resuspended in - [Read Fabrication Protocol for DNA Microarrays]

Category: PCR Protocols: cDNA Synthesis Protocols

This cDNA synthesis system simplifies your work dramatically.  All reaction components are premixed and lyophylised.  You have to add your RNA and (for Your-Prime beads) the primer.  Another advantage of the system is a little number of pipetting steps required, and therefore reduced risk of Rnase contamination and RNA degradation. - [Read First strand cDNA synthesis with Ready-To-Go Beads Protocol]

Category: Plant Biology Protocols: Arabidopsis Genetics Protocols

Forward genetics is used to identify genes that are involved in particular biological processes. For example, genes required for disease resistance can be found by identifying mutants with reduced or increased disease resistance, genes that control flower development can be identified by searching for mutants with altered flower morphology, and genes encoding enzymes for tryptophan biosynthesis can be identified by searching for mutants that require exogenous tryptophan for growth. - [Read Forward Genetics in Arabidopsis: Finding Mutations that Cause Particular Phenotypes Protocol]

Category: Competent Cells Protocols

This is an easy and straightforward protocol that gives efficiencies of 106 to 107 cfu/mg of plasmid DNA.  A growth curve is required for each strain that is prepared.
- [Read High Efficiency FCC Preparation and Tx Protocol]

Category: Immunohistochemistry Protocols

Protocol for immunohistochemistry on fixed, paraffin-embedded sections. This method is widely used and applies to the detection of the overwhelming majority of antigens, with few exceptions for which enzymatic retrieval is required. The method uses a strong chelating agent, EDTA. Includes: Double indirect AP; AP Developing solution; Indirect immunohistochemistry with avidin-biotin and HRP; HRP Developing solution. - [Read Immunohistochemistry on Fixed, Paraffin-Embedded Sections Protocol]

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]

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

LCM technology can harvest the cells of interest directly or can isolate specific cells by cutting away unwanted cells to give histologically pure enriched cell populations. A variety of downstream applications exist: DNA genotyping and loss-of-heterozygosity (LOH) analysis, etc. Protocol provides a thorough description of LCM techniques, with an emphasis on tips and troubleshooting advice derived from LCM users. The total time required to carry out this protocol is typically 1–1.5 h. - [Read Laser-capture Microdissection Protocol]

Category: Chromatography Protocols: Affinity Chromatography Protocols

Two methods are provided for purifying glycoproteins using wheat-germ agglutinin or concanavalin A-Sepharose.  Because lectin-affinity matrices can bind a few milligrams of protein per milliliter of affinity matrix, only a small amount of affinity gel matrix is required.  The batchwise method is recommended when protein volume is large. - [Read Lectin-Agarose Affinity Chromatography Protocol]

Category: Cell Culture Protocols: Cell Storing and Cell Freezing Protocols

No special treatment is required to prepare a lysate for the active collection. The following procedure should be used for long-term storage of lambda clones in the archival collections. The phage are diluted in media containing 7% DMSO and frozen at -80 degrees C. - [Read Long Term Lambda Phage Storage Protocol]

Category: Microscopy Protocols

Protocol for measuring volume. Material required includes: Microscope, Hemacytometer and coverslip, Suspension of yeast. - [Read Measuring Volume Protocol]