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Processing of Microdissected Tissue for Molecular Analysis RNA-based Studies - http://cgap-mf.nih.gov/Protocols/Processing/RNA.html

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

RNA-based studies of processing of microdissected tissue for molecular analysis. Includes: Total RNA Isolation; Optional DNAse Treatment. - [Read Processing of Microdissected Tissue for Molecular Analysis RNA-based Studies]

Production of Mouse T Cell Hybridomas Protocol - https://catalog.invitrogen.com/index.cfm?fuseaction=iProtocol.unitSectionTree&treeNodeID=9E663496BA646F5C4FB54D6064E1A19B&objectid=6674C004CF35A9AC863EAD85BD9F080A

Category: Immunology: T Cell Protocols

T cell hybridomas can be obtained by fusing activated T cells with tumor cells. A heterogeneous population of hybridomas can be cloned by limiting dilution to obtain hybridomas that express specificity to one T cell receptor (TCR). Protocol describes cell fusion and selection of T cell hybridomas. A protocol is provided for screening of T cell hybridomas for expression of the CD3-TCR complex by flow cytometry analysis. - [Read Production of Mouse T Cell Hybridomas Protocol]

Protein Isolation and Analysis From Plants - http://csm.jmu.edu/biology/courses/bio480_580/mblab/protein_isolation.htm

Category: Protein Protocols: Protein Extraction From Tissue

Protein Isolation and Analysis From Plants. T. Rife. Department of Biology, James Madison University. Harrisonburg, VA - [Read Protein Isolation and Analysis From Plants]

Protein microarray technology and ultraviolet crosslinking combined - http://www.molgen.mpg.de/~functional_protein_analysis/15265736.pdf

Category: Protein Microarray Protocols

Protein microarray technology and ultraviolet crosslinking combined with mass spectrometry for the analysis of proteinâ€“DNA interactions. Gobom. - [Read Protein microarray technology and ultraviolet crosslinking combined]

Protein Precipitation Microplate - http://www.htslabs.com/HTML/Wellplates/Applications/protein_precipitation_microplate.htm

Category: Protein Protocols: Protein Precipitation Procols

Laboratory sample cleanup is a necessary part for analytical preparation analysis. The removal of Contaminants such as proteins, cell debris and other materials is an important step. Typically this has been done by using Acetonitrile and then Centrifugation to pellet the debris leaving the clean supernant. After this process supernatant can be used for further analysis by HPLC, GC, MS and other analysis tandem methods. HTS Labs. - [Read Protein Precipitation Microplate]

Proteomic protocols and Peptide Extraction - http://www.curie.fr/recherche/themes/equipe-protocoles.cfm/id_equipe/310/lang/_gb.htm

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]

Protocol for Antiphosphotyrosine Western Blot Analysis - http://www.bio.com/protocolstools/protocol.jhtml?id=p697

Category: Signalling Signal Transduction Protocols

Detection of phosphorylated tyrosine residues can be performed using anti-P-TYR Ab and Western Analysis.Includes 2nd method,which uses phosphotyrosine in conjunction with anti-P-TYR Ab to "unlabel" potential proteins.By comparing Westerns developed with the 1st method(reveals phosphorylated protein) and the 2nd method(reveals non-specific labeling), a more accurate picture of those proteins phosphorylated on tyrosine can be seen. Includes: Protein Preparation, Electrophoresis and Transfer. - [Read Protocol for Antiphosphotyrosine Western Blot Analysis]

Protocol for Nuclear Staining of Plants for Confocal Microscopy - http://www.cshprotocols.org/cgi/content/abstract/2007/1/pdb.prot4685

Category: Microscopy Protocols: Confocal Microscopy Protocols

Protocol describes a useful way to observe the development of embryos, as well as meristems & young primordia developing at the shoot apex by confocal microscopy after staining the nuclei with propidium iodide. The number of cells can be exactly quantified in a meristem or in young primordia. Because embryonic & meristematic cells are largely filled out by their nuclei, it is easier to image only the nuclei. This method allows analysis of whole-mount material, which is more easily reconstructed. - [Read Protocol for Nuclear Staining of Plants for Confocal Microscopy]

Protocol Guide for the N. crassa Yeast Artificial Chromosome Library - http://www.fgsc.net/fgn41/yac1.html

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]

Protocols for LCM Preparation and Analysis - http://dir.nichd.nih.gov/lcm/LCMTAP.htm

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]

Protocols for Mass Spectrometry Analysis Preparation - http://www.st-andrews.ac.uk/~bmsmspf/protocols.htm#manual

Category: Mass Spectrometry Protocols

Protocols for Mass Spectrometry Analysis Preparation. Preparing gel slices for PMF or MS/MS , mass spec data interpretation, Submitting proteins in solution, Interpretation of LC-MS/MS data. BMS MASS SPECTROMETRY AND PROTEOMICS FACILITY - [Read Protocols for Mass Spectrometry Analysis Preparation]

Purification of Golgi Membranes from a Light Mitochondrial Fraction in a Self-Generated Gradient - http://www.axis-shield.com/densityhome/optiprep/S12.pdf

Category: Cell Organelle Protocols: Subcellular Fractionation Protocols: Membrane Isolation Protocols

This protocol uses a "light mitochondrial" pellet from a mammalian liver homogenate. The gradient thus has to resolve a variety of denser components (peroxisomes, lysosomes, mitochondria) from the Golgi membranes, which have a low density in iodixanol (1.06-1.09 g/ml) [1]. The protocol is specifically tailored to the purification of Golgi membranes from this pellet and is unsuitable for the isolation or analysis of other organelles present in the light mitochondrial fraction. - [Read Purification of Golgi Membranes from a Light Mitochondrial Fraction in a Self-Generated Gradient]

Purification of Peptides from Solid-Phase Peptide Synthesis with RP-HPLC Protocol - http://cshprotocols.cshlp.org/cgi/content/abstract/2006/28/pdb.prot4548

Category: Chromatography Protocols: Liquid Chromatography Protocols

Protocol details the purification and analysis of many synthetic peptides of 2-65 amino acid residues. These peptides contain a number of ionizable or polar side chains, but do not contain secondary structural elements (such as ß-sheets) that favor supramolecular assembly. - [Read Purification of Peptides from Solid-Phase Peptide Synthesis with RP-HPLC Protocol]

Quantification of DNA Methylation in Electrofluidics Chips Protocol - http://www.natureprotocols.com/2006/06/23/quantification_of_dna_methylat.php

Category: Nucleic Acid Modification Protocols: DNA Methylation Protocols

Protocol for quantification of DNA methylation in electrofluidics chips. Describe Bio-COBRA, a modified protocol for Combined Bisulfite Restriction Analysis (COBRA), that incorporates an electrophoresis step in microfluidics chips. Microfluidics technology involves the handling of small amounts of liquid in miniaturized systems. - [Read Quantification of DNA Methylation in Electrofluidics Chips Protocol]

Quick DNA Plasmid Prep. Protocol - http://genetics.med.harvard.edu/~cepko/protocol/mike/D2.html

Category: Nucleic Acid Purification Protocols: DNA Isolation Protocols: DNA Plasmid Preps Protocols

Protocol for quick DNA plasmid prep. This is a very fast mini-prep protocol which is suitable for sequence analysis and restriction digests. - [Read Quick DNA Plasmid Prep. Protocol]

Random Spore Analysis in Yeast Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/1/pdb.prot4162

Category: Yeast Cell Culture Protocols: Yeast Sporulation Protocols

Random spore analysis is used to examine meiotic recombination without performing tetrad analysis. - [Read Random Spore Analysis in Yeast Protocol]

Rapid Analysis of Bacteriophage lambda Isolates: Purification of lambda DNA from Plate Lysates - http://www.cshprotocols.org/cgi/content/extract/2006/2/pdb.prot3984

Category: Viral Manipulation Protocols: Phage Lamda Manipulation Protocols

Protocol is used to purify small amounts of bacteriophage {lambda} DNA that are suitable for use as substrates for restriction enzymes and templates for DNA and RNA polymerases. - [Read Rapid Analysis of Bacteriophage lambda Isolates: Purification of lambda DNA from Plate Lysates]

Rapid Analysis of Bacteriophage {lambda} Isolates: Purification of {lambda} DNA from Liquid Cultures - http://www.cshprotocols.org/cgi/content/extract/2006/2/pdb.prot3985

Category: Viral Culture and Isolation Protocols: Viral Culture Protocols

This protocol is used to purify small amounts of recombinant DNAs cloned in robust strains of bacteriophage {lambda} such as {lambda}gt10, {lambda}gt11, {lambda}ZAP, or ZipLox. The DNAs are suitable for use as substrates for restriction enzymes and templates for DNA and RNA polymerases. - [Read Rapid Analysis of Bacteriophage {lambda} Isolates: Purification of {lambda} DNA from Liquid Cultures]

Real-Time or Kinetic PCR - http://dna-9.int-med.uiowa.edu/realtime.htm

Category: Real Time PCR

Real-Time Chemistry, Instrumentation, Real-Time PCR Quantitation, Quantitative Primer and Probe Design, Thermal Cycling Parameters, Sample Preparation, and Real-time Data Analysis. - [Read Real-Time or Kinetic PCR]

Real-Time PCR Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/1/pdb.prot4112

Category: PCR Protocols: Real-Time PCR Protocols

Protocol uses FAM-(6-carboxy-fluorescein) or JOE-(6-carboxy-4', 5' -dichloro-2',7' -dimethoxy-fluorescein) labeled LUX (Light Upon eXtension) primers, which can quantify 100 or fewer copies of the target DNA in a background of nonspecific templates, over a broad dynamic range of less than 100-107 copies. It uses uracil deglycosylase (UDG) to minimize the risk of carryover contamination, and includes a melting curve analysis of the product. - [Read Real-Time PCR Protocol]

Removal of Genomic DNA from Total RNA for Use in Fluorescent mRNA Differential Display Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/1/pdb.prot4126

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

Protocol is the second in a set of three, describing fluorescent mRNA differential display (FDD or FDDRT-PCR). For the purposes of FDD gene expression analysis, as well as any other RNA-based gene expression technologies, contaminating genomic DNA must be removed before reverse transcription and subsequent PCR. - [Read Removal of Genomic DNA from Total RNA for Use in Fluorescent mRNA Differential Display Protocol]

Restriction Analysis of DNA Methylation Protocol - http://www.methods.info/Methods/DNA_methylation/methylation_restr.pdf

Category: Nucleic Acid Modification Protocols: DNA Methylation Protocols

Protocol for restriction analysis of DNA methylation. - [Read Restriction Analysis of DNA Methylation Protocol]

RNA (Northern) Blot Analysis Protocol - http://www.oardc.ohio-state.edu/stockingerlab/Protocols/RNAhybs.pdf

Category: Nucleic Acid Detection Protocols: Nucleic Acid Blotting Protocols

Protocol for RNA (northern) blot analysis. - [Read RNA (Northern) Blot Analysis Protocol]

RNA Preparation from Cultured Cells or Tissue Samples Protocol - http://genetics.med.harvard.edu/~cepko/protocol/mike/R2.html

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

Protocol for RNA preparation from cultured cells or tissue samples. This protocol has been used to isolate RNA from relatively small tissue samples. The RNA is clean enough for Rnase protection, cDNA synthesis, and RT-PCR analysis. - [Read RNA Preparation from Cultured Cells or Tissue Samples Protocol]

RT-PCR Analysis Protocol - http://genetics.med.harvard.edu/~cepko/protocol/mike/R4.html

Category: PCR Protocols: Reverse Transcriptase RT-PCR Protocols

Protocol for RT-PCR analysis. - [Read RT-PCR Analysis Protocol]

Articles (1-8 of 8)

Populational Analysis of Genomic DNA Protocol

A protocol on the populational Analysis of genomic DNA.

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.

Absorption Spectroscopy and Quantification of Filamentous Phage Protocol

Unlike spherical phage, such as T4 and λ, which have roughly equal weight ratios of protein to DNA, filamentous phage have about six times more protein than DNA; the protein therefore contributes substantially to the absorption spectrum.

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.

Toluidine Blue Stain

Toluidine Blue staining method and protocol for cell or tissue histology.

Thionin Stain

Thionin staining method and protocol for cell or tissue histology.

Picking Transfected ES Cell Clones Protocol

This protocol a protocol on how to generate transfected embryonic stem (ES) cell clones. The previous protocol in this series is the Protocol for Electroporation of ES cells. The next protocol in the series is the Protocol on Disaggregation, Expansion, and Freezing of Transfected ES Clones.

Vector Design Protocol for Transgenic Mice Generation

The protocol gives general considerations for the design of targeting vectors for transgenic mice. The protocol shares tips in the design of knock-out and knock-in vectors and some of their strategies for producing homologously recombined embryonic stem cells.

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