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CGH Protocols - http://amba.charite.de/cgh/protocol/02/prot02.html

Category: Cytogenetics Protocols: Comparative Genomic Hybridization CGH Protocols

A nice map linking to protocols for CGH Comparative Genomic Hybridization. Hybridization protocols, detection and analysis. Institut fÃ¼r Pathologie University Hospital CharitÃ© - [Read CGH Protocols]

CHAPOL Lineage Analyis Protocol - http://genetics.med.harvard.edu/~cepko/protocol/CHAPOL.pdf

Category: Viral Culture and Isolation Protocols: Viral Culture Protocols

Protocol for CHAPOL lineage analysis. - [Read CHAPOL Lineage Analyis Protocol]

Chromatin Immunoprecipitation and Microarray-Based Analysis of Protein Location Protocol - http://www.nature.com/nprot/journal/v1/n2/abs/nprot.2006.98.html

Category: Immunology: Immunoprecipitation Protocols: Chromatin Immunoprecipitation Protocols

Genome-wide location analysis, also known as ChIP-Chip, combines chromatin immunoprecipitation and DNA microarray analysis to identify protein-DNA interactions that occur in living cells. Protein-DNA interactions are captured in vivo by chemical crosslinking. Cell lysis, DNA fragmentation and immunoaffinity purification of the desired protein will co-purify DNA fragments that are associated with that protein. - [Read Chromatin Immunoprecipitation and Microarray-Based Analysis of Protein Location Protocol]

Chromatin Immunoprecipitation Protocol - http://www.microarrays.ca/support/PDFs/ChIP_Protocol_for_Microarray_Analysis_Beads_09-07-04.pdf#search=%22chromatin%20immunoprecipitation%20protocol%22

Category: Epigenetics and Methylation Protocols: ChIP Chromatin Immunoprecipitation Protocols

Chromatin Immunoprecipitation Protocol for Microarray Analysis â€“ Protein A/G Bead Method. UHN Microarray Centre. Brown and Farnham labs by James Paris and Mark Takahashi. - [Read Chromatin Immunoprecipitation Protocol]

Chromatin Immunoprecipitation Protocol for Microarray Analysis - http://www.microarrays.ca/support/PDFs/ChIP_Protocol_for_Microarray_Analysis_Beads_09-07-04.pdf

Category: DNA Microarray Protocols

Chromatin Immunoprecipitation Protocol for Microarray Analysis â€“ Protein A/G Bead Method. Protocol From the UHN Microarray Centre - [Read Chromatin Immunoprecipitation Protocol for Microarray Analysis]

Chromatin Immunoprecipitation Protocol PDF - http://www.microarrays.ca/support/PDFs/ChIP_Protocol_for_Microarray_Analysis_Beads_09-07-04.pdf

Category: DNA Protocols: Chromatin Immunoprecipitation Protocols

Chromatin Immunoprecipitation Protocol for Microarray Analysis â€“ Protein A/G Bead Method. Cross-Linking, Sonication/Chromatin Shearing Efficiency. Reaction UHN Microarray Centre - [Read Chromatin Immunoprecipitation Protocol PDF]

Clonality - X Chromosome Inactivation Assay Protocol - http://cgap-mf.nih.gov/Protocols/DNARNAProteomicAnalysis/DNA/DNAProtocols/Clonality.html

Category: Genetics and Genomics: Cancer Genetics Protocols

Investigators can utilize X chromosome inactivation (methylation) to determine the clonality status of a tumor or premalignant lesion in females. The technique is based on a methylation-sensitive restriction enzyme and analysis of a polymorphic locus on the X chromosome. Clonal cell populations will show "loss" of the non-methylated allele after restriction digest. The assay can be performed on DNA recovered from microdissected samples. Both frozen tissue and fixed-embedded tissue can be used. - [Read Clonality - X Chromosome Inactivation Assay Protocol]

Co-immunoprecipitation Analysis of Protein-Protein Interactions - http://www.uphs.upenn.edu/mcrc/morrisey/coip.htm

Category: Protein Protocols: Co-immunoprecipitation

Co-immunoprecipitation Analysis of Protein-Protein Interactions. Morrisey Lab - [Read Co-immunoprecipitation Analysis of Protein-Protein Interactions]

Confocal Microscopy - Simple Definitions Queens Univ. - http://meds.queensu.ca/qcri/flow/imageanalysis.htm

Category: Molecular Imaging: Confocal Microscopy Protocols and Information

Confocal Microscopy - Simple Definitions Queens Univ.Image Analysis, Co-localization Analysis, 3D Reconstruction, Object Tracking, Timelapse - Confocal, Deconvolution. - [Read Confocal Microscopy - Simple Definitions Queens Univ.]

Construction of Genomic DNA Libraries in Cosmid Vectors Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/2/pdb.prot4000

Category: DNA Protocols: Cosmid Library Protocols

Protocol describes how to construct a library of 35-45-kb fragments of genomic DNA in the double cos site cosmid vector, SuperCos-1. The steps include: Linearization and dephosphorylation of SuperCos-1 DNA; Partial digestion of high-molecular-weight DNA with MboI; Dephosphorylation of high-molecular-weight genomic DNA; Ligation of cosmid arms to genomic DNA: Packaging and plating recombinants; Isolation and analysis of recombinant cosmids: Validation of the library. - [Read Construction of Genomic DNA Libraries in Cosmid Vectors Protocol]

Cytochrome Oxidase Manometric Analysis - http://homepages.gac.edu/~cellab/chpts/chpt8/ex8-6.html

Category: Plant Biology Protocols: Photosynthesis and Respiration Protocols

Protocol describing cytochrome oxidase manometric analysis. Protocol includes: Manometric Analysis and information on the the Gilson Constant Pressure Respirometer. - [Read Cytochrome Oxidase Manometric Analysis]

Detection of Chromosomal Imbalances Using DOP-PCR and Comparative Genomic Hybridization (CGH) - http://www.roche-applied-science.com/PROD_INF/MANUALS/InSitu/pdf/ISH_95-103.pdf

Category: Cytogenetics Protocols

CGH provides a comprehensive picture of all chromosomal gains and losses within a single experiment. In contrast to banding analysis, CGH requires no preparation of metaphase chromosomes from the cells to be analyzed (which in certain tumor types may be difficult or even impossible). - [Read Detection of Chromosomal Imbalances Using DOP-PCR and Comparative Genomic Hybridization (CGH)]

Dissection of Spinal Cords for Analysis of Axonal Pathfinding in dsRNA Treated Avian Embryos - http://www.cshprotocols.org/cgi/content/abstract/2006/23/pdb.prot4505

Category: RNAi Technology Protocols: RNAi Avian Embryos Protocols

Protocol describes how to dissect spinal cords of dsRNA-treated avian embryos for analysis of commissural axon guidance. After fixation of the spinal cord with paraformaldehyde, commissural axons are stained with Fast-DiI. - [Read Dissection of Spinal Cords for Analysis of Axonal Pathfinding in dsRNA Treated Avian Embryos]

Dissection of Spinal Cords for Analysis of Axonal Pathfinding in dsRNA-Treated Avian Embryos - http://www.cshprotocols.org/cgi/content/abstract/2006/23/pdb.prot4505

Category: Avian Bird Protocols

DNA Analysis by Flow Cytometry Protocol - http://www.niehs.nih.gov/research/atniehs/core/fc/protocols/dna.cfm

Category: Cell Biology and Cell Culture: Flow Cytometry Protocols

Protocol for DNA analysis by flow cytometry. - [Read DNA Analysis by Flow Cytometry Protocol]

Embryo Lysates & Immunoprecipitation Protocol - http://spot.colorado.edu/~klym/Methods/Precipitation.htm

Category: Xenopus Protocols: Xenopus Embryo Manipulation Protocols

Protocol for embryo lysates and immunoprecipitation: protein A agarose & protein A magnetic beads. Includes: Embryo lysates; Immunoprecipitation with protein A agarose; Immunoprecipitation with protein A magnetic beads for silver stain/sequencing analysis. - [Read Embryo Lysates & Immunoprecipitation Protocol]

Epitope Mapping by Competition Assay Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/18/pdb.prot4277

Category: Antibody Protocols: Epitope Mapping Antibody Protocols

The simplest way to determine whether two monoclonal antibodies bind to distinct sites on a protein antigen is to carry out a competition assay. The assay can be used with antibodies that bind both conformational and linear epitopes, and it is most useful in the analysis of monoclonal antibody specificity because polyclonal sera typically recognize multiple different epitopes. - [Read Epitope Mapping by Competition Assay Protocol]

ES mouse cell stem cell Culture - http://imgen.bcm.tmc.edu/dtmc/mouse_embryonic_stem_cell_culture.html

Category: Cell Biology and Cell Culture: ES Stem Cell Biology and Culture

Mouse Embryonic Stem Cell Culture. Southern Analysis of ES cells. The Darwin Transgenic Core Facility - [Read ES mouse cell stem cell Culture]

Extraction and analysis of diagnostically useful proteins from formalin-fixed, paraffin-embedded tis - http://www.jhc.org/cgi/content/full/46/3/397

Category: Protein Protocols: Protein Extraction From Tissue

Extraction and analysis of diagnostically useful proteins from formalin-fixed, paraffin-embedded tissue sections. Ikedaa et al, 1998 JHC. - [Read Extraction and analysis of diagnostically useful proteins from formalin-fixed, paraffin-embedded tis]

FASC Analysis of Cell Cycle using BrdU and PI Protocol - http://www.niehs.nih.gov/research/atniehs/core/fc/protocols/fasc.cfm

Category: Cell Biology and Cell Culture: Flow Cytometry Protocols

Protocols for FASC analysis of cell cycle using BrdU and PI. Includes: Labeling of Cells with BrdU; Collecting the Cells; Processing the Cells. - [Read FASC Analysis of Cell Cycle using BrdU and PI Protocol]

FDD PCR, Identification and Analysis of Differentially Expressed cDNAs Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/14/pdb.prot4128

Category: PCR Protocols

Protocol for FDD PCR, identification and analysis of differentially expressed cDNAs. - [Read FDD PCR, Identification and Analysis of Differentially Expressed cDNAs Protocol]

FIXATION and DNA Staining for Cell Cycle Analysis - http://www.biotech.iastate.edu/facilities/CELLHYB/CCAnalysis.htm

Category: Cell Biology and Cell Culture: Flow Cytometry Protocols

FIXATION and DNA Staining for Cell Cycle Analysis Protocol. This method of DNA staining utilizes ethanol to fix the cells and permeabilize the membrane, which allows the dye (Propidium Iodide) to enter the cells. Propidium Iodide (PI) is a DNA-binding fluorochrome that intercalates in the double-helix. Ribonuclease-A is used to eliminate the staining of double-stranded RNA. - [Read FIXATION and DNA Staining for Cell Cycle Analysis]

FIXATION PROTOCOL FOR FLOW CYTOMETRIC ANALYSIS OF DNA BY PI STAINING - http://www.vetmed.auburn.edu/index.pl/cell_cycle/dna_content

Category: Histology Protocols: Fixation of Cells Tissues Protocol

Analysis of Cell Cycle Based on DNA Content. FIXATION PROTOCOL FOR FLOW CYTOMETRIC ... Liberate cells from tissue culture flask by trypsin digestion and ... FIXATION PROTOCOL FOR FLOW CYTOMETRIC ANALYSIS OF DNA BY PI STAINING. Auburn University, College of Veterinary Medicine. You. - [Read FIXATION PROTOCOL FOR FLOW CYTOMETRIC ANALYSIS OF DNA BY PI STAINING]

Flow Cytometric Analysis of Gram-Negative Bacterial Cells - http://www.cyto.purdue.edu/flowcyt/research/micrflow/robert/robert.htm

Category: Cell Biology and Cell Culture: Flow Cytometry Protocols

Flow cytometric analysis of gram-negative bacterial cells. Includes: Staining Conditions and FACSort Settings; Light Scatter Resolution on the BD FACSort; Bacterial Cell Resolution on the BD FACSort. - [Read Flow Cytometric Analysis of Gram-Negative Bacterial Cells]

Flow Cytometric Analysis of Mitochondrial Transmembrane Potential ({Delta}{Psi}m) - http://www.cshprotocols.org/cgi/content/extract/2006/21/pdb.prot4465

Category: Cell Organelle Protocols: Mitochondria Protocols

Protocol describes a method for evaluation of mitochondrial function using the fluorochrome CMXRos. CMXRos is sequestered by actively respiring mitochondria, but washed out when the mitochondrial membrane potential is lost. This analysis can be combined with the TUNEL technique or immunocytochemistry. - [Read Flow Cytometric Analysis of Mitochondrial Transmembrane Potential ({Delta}{Psi}m)]

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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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