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1,115 Newest Publications in csh protocols


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01-May-2018 | Kim, T. H., Dekker, J., CSH Protocols, 2018

ChIP-chip can be used to analyze protein–DNA interactions in a region-wide and genome-wide manner. DNA microarrays contain PCR products or oligonucleotide probes that are designed to represent genomic sequences. Identification of genomic sites that interact with a specific protein is based on ...


Touchdown Polymerase Chain Reaction (PCR)

01-May-2018 | Green, M. R., Sambrook, J., CSH Protocols, 2018

"Touchdown polymerase chain reaction (PCR)" is a method to decrease off-target priming and hence to increase the specificity of PCRs. In touchdown PCR the temperature selected for the annealing step is initially set 5°C–10°C higher than the calculated Tm of the primers. Annealing under conditions ...


Hot Start Polymerase Chain Reaction (PCR)

01-May-2018 | Green, M. R., Sambrook, J., CSH Protocols, 2018

The purpose of hot start polymerase chain reaction (PCR) is to optimize the yield of the desired amplified product in PCRs and, simultaneously, to suppress nonspecific amplification and formation of primer dimers. This is achieved by withholding an essential component of the PCR—the DNA ...


Making Weak Antigens Strong: Modifying Protein Antigens by Denaturation

01-May-2018 | Greenfield, E. A., DeCaprio, J., Brahmandam, M., CSH Protocols, 2018

Many molecules can be made more immunogenic by denaturation. This treatment will change the structure of many compounds, particularly proteins, and expose new epitopes. In addition, heating will often cause protein antigens to aggregate, and, because aggregated antigens are often more ...


Mouse Embryo Cryopreservation by Rapid Cooling

01-May-2018 | Shaw, J., CSH Protocols, 2018

Embryo cryopreservation has been used to archive mouse strains. Protocols have evolved over this time and now vary considerably in terms of cryoprotectant solution, cooling and warming rates, methods to add and remove cryoprotectant, container or carrier type, volume of cryoprotectant, the stage ...


Mouse Embryo Cryopreservation by Slow Freezing

01-May-2018 | Taft, R., CSH Protocols, 2018

This embryo cryopreservation protocol is used by The Jackson Laboratory and several other repositories around the world. This protocol has clearly withstood the test of time; >2 million embryos from thousands of strains have been cryopreserved using this method. It requires a controlled-rate ...


ChIP-Quantitative Polymerase Chain Reaction (ChIP-qPCR)

01-May-2018 | Kim, T. H., Dekker, J., CSH Protocols, 2018

It is critical to determine if the ChIP actually enriched the DNA sequences that are associated with the target protein. If there are known genomic binding sites, primers can be designed for quantitative PCR (qPCR) to determine if the known sites are specifically enriched by immunoprecipitation. ...


Subcutaneous Injection of Pluripotent Stem Cells in Mice

01-Apr-2018 | Nagy, K. V., Nagy, A., CSH Protocols, 2018

This protocol describes the production of teratomas and teratocarcinomas used to determine the in vivo developmental potential of adult or embryonic tissues, including early-stage embryos, somites, and tail bud, as well as embryonic and other pluripotent stem cells. Resulting tumors are screened ...


Titration of Lentivirus Vectors

01-Apr-2018 | Sena-Esteves, M., Gao, G., CSH Protocols, 2018

The titer of a lentivirus vector is often expressed in transducing units per milliliter. This is a functional titer that reflects the lentivirus’ ability to transduce a particular cell line under specific conditions. Transduction of other cell lines is likely to be different and will require ...


Formaldehyde Cross-Linking

01-Apr-2018 | Kim, T. H., Dekker, J., CSH Protocols, 2018

Formaldehyde cross-linking of DNA to associated proteins is a relatively straightforward method, but it is also the most critical step in the chromatin immunoprecipitation (ChIP) and 3C analyses. Although formaldehyde is a highly permeable cross-linker, its maximum cross-linking efficiencies are ...


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