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In Situ Methods to Localize Transgenes and Transcripts in Interphase Nuclei - http://www.plantmethods.com/content/2/1/18

Category: Cytogenetics Protocols: In Situ Hybridization Protocols

In situ methods to visualize transgenes (including single copy genes) and their transcripts during interphase from different tissues and plant species. These techniques reduce the time necessary for characterization of transgene integration by eliminating the need for time-consuming segregation analysis, and extend characterization to the interphase nucleus, thus increasing the likelihood of accurate prediction of transgene activity. - [Read In Situ Methods to Localize Transgenes and Transcripts in Interphase Nuclei]

In-gel digestion of proteins for peptide fingerprint mapping - http://www.bio.vu.nl/vakgroepen/mnb/proteomics/6.in-geldigestion.html

Category: Mass Spectrometry Protocols

Peptide Mapping Analysis Techniques. Dr.Aebersold, Vrije Universiteit Amsterdam - [Read In-gel digestion of proteins for peptide fingerprint mapping]

In-gel digestion of proteins to be analyzed by mass spectrometry - http://www.narrador.embl-heidelberg.de/GroupPages/PageLink/activities/protocols/ingeldigest.html

Category: Proteomic Protocols

In-Gel Digestion Protocol. Excision of protein bands (spots) from polyacrylamide gels Reduction and alkylation . Reduction and alkylation . MALDI analysis of the supernatant after in-gel digestion. Extraction of Peptides.Matthias Wilm EMBL Bioanalytical R - [Read In-gel digestion of proteins to be analyzed by mass spectrometry]

Intracellular Staining for Flow Cytometric Analysis Protocols - http://www.ebioscience.com/ebioscience/appls/FCI.htm?

Category: Signalling Signal Transduction Protocols: Cytokine Protocols

Intracellular Cytokine Staining Protocol. Analysis of surface molecules and intracellular cytokines at the single-cell level using FACS or flow cytometry. - [Read Intracellular Staining for Flow Cytometric Analysis Protocols]

Isolating Germ Cells from the Genital Ridge - http://www.cshprotocols.org/cgi/content/extract/2006/1/pdb.prot4370

Category: Mouse Protocols: Mouse Cell Culture Protocols

Protocol describes isolation of germ cells from the genital ridge of fetal mice from 11.5 days post coitum (dpc) onward. The germ cells can then be used for analysis, culture, or transplantation. - [Read Isolating Germ Cells from the Genital Ridge]

Isolating Germ Cells from the Genital Ridge Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/1/pdb.prot4370

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

This protocol describes isolation of germ cells from the genital ridge of fetal mice from 11.5 days post coitum (dpc) onward. The germ cells can then be used for analysis, culture, or transplantation. - [Read Isolating Germ Cells from the Genital Ridge Protocol]

Isolation of Arabidopsis cDNAs by Complementation in Yeast - http://www.arabidopsis.org/cshl-course/12-yeast.html

Category: Plant Biology Protocols: Arabidopsis Nucleic Acid Protocols

Includes: Isolation of Arabidopsis LEU2 cDNAs by complementation of the yeast leu2 mutation; Recovery of plasmid DNA from yeast cells; Analysis of Arabidopsis cDNAs that complement a yeast leu2 mutation; Preparation of library DNA from the Lacroute cDNA library; Preparation of Yeast Media. - [Read Isolation of Arabidopsis cDNAs by Complementation in Yeast]

Isolation of DNA from Mammalian Cells Grown in 96-well Microtiter Plates Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/2/pdb.prot3695

Category: Nucleic Acid Purification Protocols: DNA Isolation Protocols: Genomic DNA Isolation Protocols

Protocol for isolation of DNA from mammalian cells grown in 96-well microtiter plates. Each well yields sufficient genomic DNA for several standard PCRs or for analysis in a single lane of a Southern hybridization. - [Read Isolation of DNA from Mammalian Cells Grown in 96-well Microtiter Plates Protocol]

Isolation of Yeast Genomic DNA for Southern Blot Analysis Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/1/pdb.prot4149

Category: Yeast Protocols: Yeast Nucleic Acid Protocols: Yeast DNA Isolation Protocols

Protocol (modified from Hoffman and Winston 1987) describes the purification of genomic DNA from yeast cells. - [Read Isolation of Yeast Genomic DNA for Southern Blot Analysis Protocol]

Kinase Assay Using In Vitro Translated Xenopus Mos Kinase - http://www.bio.com/protocolstools/protocol.jhtml?id=p912

Category: Signalling Signal Transduction Protocols

Protocol describes how tagged Mos kinase is translated in vitro, immunopurified, and used in a kinase assay. Protocol includes: Translation of Xenopus Mos Kinase; Antibody to Antigen Binding; Protein A Sepharose to Antibody Binding; Kinase Reactions on Immunoprecipitated Material; Polyacrylamide Gel Analysis of Immunoprecipitates. Includes protocol hints. - [Read Kinase Assay Using In Vitro Translated Xenopus Mos Kinase]

Laser-capture Microdissection Protocol - http://www.nature.com/nprot/journal/v1/n2/full/nprot.2006.85.html#a1

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]

Lineage Analysis Using Retroviral Vectors - http://genetics.med.harvard.edu/~cepko/lineage/

Category: Developmental Biology

Describe the use of replication-incompetent retroviral vectors for the analysis of lineal relationships in developing vertebrate tissues. An overview of the relevant aspects of the retroviral life cycle, and the strategies and current methods in use at their laboratory are described. - [Read Lineage Analysis Using Retroviral Vectors]

Lineage Analysis Using Retroviral Vectors Protocol - http://genetics.med.harvard.edu/~cepko/lineage/

Category: Cloning Protocols: Vector Protocols

Protocol describes the use of replication-incompetent retroviral vectors for the analysis of lineal relationships in developing vertebrate tissues. - [Read Lineage Analysis Using Retroviral Vectors Protocol]

Linkage Analysis Using the NaOH Methylation Method Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/1/pdb.prot4249

Category: Chromatography Protocols: Gas Chromatography Protocols

Linkage analysis provides information on sugar type, ring size, and substitution positions for each monosaccharide. The method in this protocol, using NaOH as the base, is one of the simpler linkage analysis methods. It requires approximately 1-5 µg of carbohydrate. - [Read Linkage Analysis Using the NaOH Methylation Method Protocol]

Lipid Analysis Protocol - http://www.sfu.ca/bisc/bisc-429/transmethylation.html

Category: Lipid Protocols

Protocol for lipid analysis. - [Read Lipid Analysis Protocol]

Lipid Analysis Using Thin Layer Chromotography Protocol - http://www.sfu.ca/bisc/bisc-429/TLC.html

Category: Lipid Protocols

Protocol for lipid analysis using thin layer chromotography. Protocol includes: Thin layer chromatography: Absorbent: Solvents, Development and Visualization. - [Read Lipid Analysis Using Thin Layer Chromotography Protocol]

Live Imaging of Caenorhabditis elegans: Preparation of Samples - http://www.cshprotocols.org/cgi/content/abstract/2006/29/pdb.prot4601

Category: Microscopy Protocols: In Vivo Imaging Protocols

Caenorhabditis elegans, a small (adults are ~1 mm long), free-living soil nematode that feeds on bacteria, is an ideal organism for applying various live microscopy techniques. This protocol describes useful techniques for preparing C. elegans for live microscopic analysis. Details of sample preparation depend on the developmental stage of the worm to be studied. - [Read Live Imaging of Caenorhabditis elegans: Preparation of Samples]

Live Imaging of Caenorhabditis elegans: Preparation of Samples - http://www.cshprotocols.org/cgi/content/abstract/2006/29/pdb.prot4601

Category: C. elegans Protocols

Protocol describes useful techniques for preparing C. elegans for live microscopic analysis. Details of sample preparation depend on the developmental stage of the worm to be studied. - [Read Live Imaging of Caenorhabditis elegans: Preparation of Samples]

Live/Dead Assay for Cell Viability Protoco - http://www.signaling-gateway.org/data/cgi-bin/ProtocolFile.cgi/afcs_PP00000023.pdf?pid=PP00000023

Category: Cell Biology and Cell Culture: Cell Viability Protocols

Assay measures cell viability. It is a two-color fluorescence assay that simultaneously determines Live cell number and Dead cell number. This protocol is designed for use with the GEMINI XS Microplate Spectrofluorometer, a multi-well plate scanner with dual excitation/emission capabilities, but the assay is also adaptable for flow cytometry and fluorescence microscopy. Includes: Cell Culture; Preparation for the Assay; Live/Dead Assay; Reading the Plate; Data Analysis; Alternative protocol. - [Read Live/Dead Assay for Cell Viability Protoco]

Luciferase Assay 24 Well Plate (Promega System) - http://www.biochem.northwestern.edu/ibis/morimoto/research/Protocols/II.%20Eukaryotes/F.%20Luciferase%20Assays/2a.single%20luciferase.pdf

Category: Reporter Gene Assays: Luciferase Assay Protocols

Luciferase assay using a 24 well plate. Includes: Cell Lysis; Reagent Preparation; Luminescence measurement; Wash injector; Protein quantitation; Data Analysis. - [Read Luciferase Assay 24 Well Plate (Promega System)]

M5 Velocity (rate zonal) gradients for purification and assembly analysis of viruses. - http://www.axis-shield.com/densityhome/optiprep/M05.pdf

Category: Cell Biology and Cell Culture

Purification protocols of the viruses: HIV-1, Lassa virus, oncornavirus and other retroviruses. Protocol uses an iodixanol gradient in a sedimentation velocity mode to purifyHIV-1 virions without affecting the infectivity of the virus. In rate-zonal iodixanol gradients the HIV-1 was effectively separated both from Vif and from the microvesicles. - [Read M5 Velocity (rate zonal) gradients for purification and assembly analysis of viruses.]

MALDI Matrices - http://www.narrador.embl-heidelberg.de/GroupPages/PageLink/activities/protocols/maldimatrices.html

Category: Mass Spectrometry Protocols

MALDI Matrices. Commonly used MALDI matrices for analysis of peptides, proteins, carbohydrates, and nucleic acids using 337 nm or 355 nm UV lasers. All matrices can be used for sample preparation using the Dried Droplet Method whereas only matrices solubl - [Read MALDI Matrices]

Mammalian Cell Culture and Preparation of Cells for RNAi in 24-Well Plates Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/1/pdb.prot4341

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

This protocol introduces a method for maintaining mammalian cell culture suitable for treatment with siRNA. Transfection of cultured cells with siRNAs (see Transfection of siRNA Duplexes into Mammalian Cells) and downstream analysis of the knockdown cells. - [Read Mammalian Cell Culture and Preparation of Cells for RNAi in 24-Well Plates Protocol]

Mammalian Cell Culture and Preparation of Cells for RNAi in 24-Well Plates Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/1/pdb.prot4341

Category: RNAi Technology Protocols: RNAi Mammalian Cells Protocols

Protocol introduces a method for maintaining mammalian cell culture suitable for treatment with siRNA. Transfection of cultured cells with siRNAs and downstream analysis of the knockdown cells. - [Read Mammalian Cell Culture and Preparation of Cells for RNAi in 24-Well Plates Protocol]

Mass spectrometry analysis and identification of proteins - http://www.healthsystem.virginia.edu/internet/biomolec/mass_spectrometry.cfm

Category: Mass Spectrometry Protocols

Protein sequencing by mass spectrometry. Mass analysis of peptides and proteins. Identification of modifications in proteins. Good information.Univ. Virginia. Dr. Nicholas Sherman - [Read Mass spectrometry analysis and identification of proteins]

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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