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Neural Stem Cell Culture: Neurosphere Generation, Microscopical Analysis and Cryopreservation - http://www.natureprotocols.com/2006/08/25/neural_stem_cell_culture_neuro.php

Category: Stem Cell Protocols: Stem Cell Culture Protocols

Describes the steps in detail to isolate and expand neural stem cells in the form of neurospheres from tissue dissections of the post-natal mouse brain. Procedures for the long term passage of neurospheres and the cryopreservation of neurospheres are also provided. In addition to the guidelines and tips for generating neurosphere cultures, we describe the method to prepare neurospheres for analysis by light microscopy. - [Read Neural Stem Cell Culture: Neurosphere Generation, Microscopical Analysis and Cryopreservation]

NIH Image for Mac - http://rsb.info.nih.gov/nih-image/

Category: Molecular Imaging

NIH Image. Image can be used to measure area, mean, centroid, perimeter, etc. of user defined regions of interest. It also performs automated particle analysis and provides tools for measuring path lengths and angles. Spatial calibration is supported to p - [Read NIH Image for Mac]

Non-linear Regression Programs for the Analysis of Pharmacokinetic and Pharmacodynamic Data - http://www.boomer.org/manual/toc.html

Category: Pharmacology and Toxicology Protocols: Pharmacokinetics Protocols

Non-linear Regression Programs for the Analysis of Pharmacokinetic and Pharmacodynamic Data - [Read Non-linear Regression Programs for the Analysis of Pharmacokinetic and Pharmacodynamic Data]

Northern Blot Analysis of mRNA From Mammalian Polyribosomes Protocol - http://www.natureprotocols.com/2006/09/15/northern_blot_analysis_of_mrna.php

Category: Nucleic Acid Detection Protocols: Nucleic Acid Blotting Protocols

The protocol consists of a method for the generation of cytoplasmic extracts from mammalian cells (in this case, 293T cells) without the disruption of polyribosomes, the separation of ribosomal components and polyribosomes by sucrose gradient centrifugation, the isolation of mRNA from these fractions, and detection of mRNA by Northern blot analysis. - [Read Northern Blot Analysis of mRNA From Mammalian Polyribosomes Protocol]

Partial Mouse Hepatectomy Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/18/pdb.prot4384

Category: Mouse Protocols: Mouse Organ Removal Surgery Protocols

Protocol describes partial removal of a mouse liver to provide tissue for analysis. - [Read Partial Mouse Hepatectomy Protocol]

PCR Analysis of Agrobacterium Protocol - http://www.cshprotocols.org/cgi/content/abstract/2006/30/pdb.prot4667

Category: Bacteria Genetics Protocols

Protocol describes a method to determine the presence of plasmid DNA in an Agrobacterium culture. Compared to selection of transformed Agrobacterium, which can be ambiguous and normally takes several days for resistant colonies to appear, the approach described here is both rapid and accurate. - [Read PCR Analysis of Agrobacterium Protocol]

Phosphoamino acid analysis - http://pingu.salk.edu/~sefton/Hyper_protocols/Paa.html

Category: Protein Protocols: Protein Phosphorylation Protocols

Recipes and protocols for the analysis of phosphoamino acids (PAA). Mark Kamps's method. Bart's Cookbook. - [Read Phosphoamino acid analysis]

Phosphoamino acid analysis of non-TCA precipitable proteins - http://kinase.uhnres.utoronto.ca/methods/PAA.html

Category: Protein Protocols: Protein Quantitation Concentration Protocols

Phosphoamino acid analysis of non-TCA precipitable proteins and Alkali treatment of gels protocols. Woodgett Lab. - [Read Phosphoamino acid analysis of non-TCA precipitable proteins]

Plant Protein Isolation - http://www.oardc.ohio-state.edu/stockingerlab/Protocols/ProteinIsolation.pdf

Category: Protein Protocols: Protein Extraction From Tissue

Plant Protein Isolation - Rapid isolation of protein for SDS-PAGE analysis. (Essentially the same protocol as that described for GUS Assays). Stockinger Lab - [Read Plant Protein Isolation]

Plasmid Isolation and Analysis. Pictorial Protocol. - http://www.biotech.iastate.edu/publications/ppt_presentations/html/IsoPart1_files/v3_document.htm

Category: General Research Protocols and Methods

Plasmid Isolation and Analysis. Pictorial Protocol. Mike Zeller. - [Read Plasmid Isolation and Analysis. Pictorial Protocol.]

Preparation and LCM of Paraffin Embedded Tissue Sections Protocol - http://dir.nichd.nih.gov/lcm/LCMTAP.htm#II.%20Preparation%20and%20LCM%20of%20Paraffin%20Embedded%20Tissue%20Sections

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]

Preparation of a Denaturing Agarose Gel for the Analysis of RNA Samples Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/14/pdb.prot4127

Category: Nucleic Acid Electrophoresis Protocols: RNA Electrophoresis Protocols

Protocol for preparation of a denaturing agarose gel for the analysis of RNA samples. The integrity of RNA samples can be analyzed by electrophoresis on a denaturing agarose gel containing formaldehyde. - [Read Preparation of a Denaturing Agarose Gel for the Analysis of RNA Samples Protocol]

Preparation of B-Lymphocyte RNA for Microarray Analysis Protocol - http://www.signaling-gateway.org/data/cgi-bin/ProtocolFile.cgi/afcs_PP00000009.pdf?pid=PP00000009

Category: Immunology: B Cell Protocols

Procedure permits the isolation of at least 5 µg of total RNA from a sample of purified mouse splenic B lymphocytes. The quality of the RNA is assessed by separation of an aliquot through 1% agarose and staining with ethidium bromide as described in AfCS protocol Visualization of RNA Preparations on 1% Agarose Gels. The isolated RNA is used for analysis of gene expression by microarray technology. analysis of gene expression by microarray technology. - [Read Preparation of B-Lymphocyte RNA for Microarray Analysis Protocol]

Preparation of B-Lymphocyte RNA for Microarray Analysis Protocol - http://www.signaling-gateway.org/data/cgi-bin/ProtocolFile.cgi/afcs_PP00000009.pdf?pid=PP00000009

Category: Microarray Protocols: Microarray Analysis Protocols

Protocol permits the isolation of at least 5 µg of total RNA from a sample of purified mouse splenic B lymphocytes Isolation of Resting B Lymphocytes from Sixteen Mouse Spleens. - [Read Preparation of B-Lymphocyte RNA for Microarray Analysis Protocol]

Preparation of Brain Membrane Fractions for Western Blot Analysis - http://www.bdbiosciences.com/pharmingen/protocols/Brain_Membrane_Fractions.shtml

Category: Protein Protocols: Western Blot Protocol

Western blotting using enriched membrane preparation and postsynaptic densities are desired. (BD Biosciences) - [Read Preparation of Brain Membrane Fractions for Western Blot Analysis]

Preparation of Cells and Reagents for Flow Cytometry Protocols - https://catalog.invitrogen.com/index.cfm?fuseaction=iProtocol.unitSectionTree&treeNodeID=9E661C3CC685613447CEC768412FDE0F&objectid=6674EA50F5C3D9A0189B376C7A89BF6B

Category: Cell Biology and Cell Culture: Flow Cytometry Protocols

A procedure for direct and indirect staining of single-cell suspensions of lymphoid tissue or peripheral blood lymphocytes to detect cell surface membrane antigens is presented. In addition, support protocols present methods for fluorescence labeling of purified antibodies. A protocol for flow cytometric analysis of intracellular antigens in single-cell suspensions is also included. - [Read Preparation of Cells and Reagents for Flow Cytometry Protocols]

Preparation of metaphase chromosomes from lymphoblastoid cell lines - http://www.sanger.ac.uk/HGP/methods/cytogenetics/metaphase.shtml

Category: Cytogenetics Protocols: Fluorescent In Situ Hybridization FISH Protocol

Preparation of metaphase chromosomes from lymphoblastoid cell lines for FISH analysis. Sanger Institue. - [Read Preparation of metaphase chromosomes from lymphoblastoid cell lines]

Preparation of Myocyte RNA for Microarray Analysis Protocol - http://www.signaling-gateway.org/data/cgi-bin/ProtocolFile.cgi/afcs_PP00000133.pdf?pid=PP00000133

Category: Microarray Protocols: Microarray Analysis Protocols

Protocol permits the isolation of at least 3 µg of total RNA from approximately 150,000 cultured cardiac myocytes from adult mice. Includes: Treatment of Samples and Termination of Reactions; Isolation of RNA; Use of Environmental Chamber. - [Read Preparation of Myocyte RNA for Microarray Analysis Protocol]

Preparation of Protein Extracts for 2D Gel-analysis - http://www.riedlab.nci.nih.gov/publications/2425.1533_2D_Gel_Protein_Ext.pdf

Category: Protein Protocols: Protein Extraction From Cells

Preparation of Protein Extracts for 2D Gel-analysis. Thomas Ried Lab NCI. - [Read Preparation of Protein Extracts for 2D Gel-analysis]

Preparing Cells for PI/FACS (cell cycle) Analysis Protocol - http://www.flemingtonlab.com/Protocols/PreparingCellsforFACS-PI.pdf

Category: Cell Biology and Cell Culture: Cell Cycle Protocols

This method works well to assess cell cycle distribution of whole cell populations. This method can also be used to assess the cell cycle distribution of GFP transfected cells however, the EtOH step is generally not sufficient to keep GFP in the cell. - [Read Preparing Cells for PI/FACS (cell cycle) Analysis Protocol]

Preparing Cells for PI/FACS (cell cycle) Analysis Protocol - http://www.flemingtonlab.com/Protocols/PreparingCellsforFACS-PI.pdf

Category: Cell Biology and Cell Culture: Flow Cytometry Protocols: Cell Cycle Analysis Protocols

Protocol for preparing cells for PI/FACS (cell cycle) analysis. - [Read Preparing Cells for PI/FACS (cell cycle) Analysis Protocol]

Preparing Cells for PI/FACS (cell cycle) Analysis Protocol - http://www.flemingtonlab.com/Protocols/PreparingCellsforFACS-PI.pdf

Category: Cell Biology and Cell Culture: Flow Cytometry Protocols: Flow Cytometry Data Analysis Protocols

Protocol for preparing cells for PI/FACS (cell cycle) analysis. - [Read Preparing Cells for PI/FACS (cell cycle) Analysis Protocol]

Probing Protein Interactions Using GFP and FRET Protocol - http://www.cshprotocols.org/cgi/content/extract/2006/2/pdb.prot3893

Category: Reporter Gene Assays: GFP Assay Protocols

In preparation for FLIM-FRET analysis, the appropriate donor and acceptor components must be introduced into live or fixed cells. The method of introduction depends on the nature of the components and the state of the cells. For example, plasmid DNAs encoding a protein of interest fused to a variant of GFP may be introduced into live cells by transfection or microinjection, whereas labeled antibodies are delivered by microinjection. - [Read Probing Protein Interactions Using GFP and FRET Protocol]

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

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

Information on processing of microdissected tissue for molecular analysis. Includes: More than 10,000 Cells; Less than 10,000 Cells; Formalin-fixed; Paraffin-embedded Tissue; Other Fixatives; Timing. - [Read Processing of Microdissected Tissue for Molecular Analysis]

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

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

The methodology and buffers utilized for processing microdissected samples for protein-based studies is variable depending on the downstream molecular analysis method. - [Read Processing of Microdissected Tissue for Molecular Analysis Proteomics-based Studies]

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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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