Show simple item record

dc.contributor.authorKim, Tae Hoon
dc.contributor.authorDekker, Job
dc.date2022-08-11T08:10:59.000
dc.date.accessioned2022-08-23T17:27:29Z
dc.date.available2022-08-23T17:27:29Z
dc.date.issued2018-09-04
dc.date.submitted2018-12-06
dc.identifier.citation<p>Cold Spring Harb Protoc. 2018 Sep 4;2018(9):pdb.prot097873. doi: 10.1101/pdb.prot097873. <a href="https://doi.org/10.1101/pdb.prot097873">Link to article on publisher's site</a></p>
dc.identifier.issn1559-6095 (Linking)
dc.identifier.doi10.1101/pdb.prot097873
dc.identifier.pmid30181221
dc.identifier.urihttp://hdl.handle.net/20.500.14038/49874
dc.description.abstractIn all 3C-based assays, the aim is to measure the frequency with which two loci interact within cells. This is achieved by determining the relative abundance of ligation products formed during the 3C protocol that carry sequences from both loci. Individual 3C ligation products that are present in a 3C library, the ChIP-loop library, or the control library can be detected by polymerase chain reaction (PCR) using locus-specific primers. The following protocol outlines the procedure to measure relative abundances of ligation products in these libraries using PCR. The first part of the protocol-library titration-is required only once to determine the linear range of PCR detection. Once the linear range of PCR detection is known for a given ligation product library, follow the second part-interaction analysis-to measure the abundance of ligation products of interest in that library. Specific issues regarding determining the relative abundance of ligation products, designing PCR primers, and quantifying interaction frequencies are also described.
dc.language.isoen_US
dc.relation<p><a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&list_uids=30181221&dopt=Abstract">Link to Article in PubMed</a></p>
dc.relation.urlhttps://doi.org/10.1101/pdb.prot097873
dc.subjectBiochemistry
dc.subjectGenetic Phenomena
dc.subjectGenetics and Genomics
dc.subjectInvestigative Techniques
dc.subjectLaboratory and Basic Science Research
dc.subjectMolecular Biology
dc.subjectSystems Biology
dc.titlePolymerase Chain Reaction (PCR) Detection of 3C Ligation Products Present in 3C, ChIP-Loop, and Control Libraries: Library Titration and Interaction Frequency Analysis
dc.typeJournal Article
dc.source.journaltitleCold Spring Harbor protocols
dc.source.volume2018
dc.source.issue9
dc.identifier.legacycoverpagehttps://escholarship.umassmed.edu/sysbio_pubs/146
dc.identifier.contextkey13437611
html.description.abstract<p>In all 3C-based assays, the aim is to measure the frequency with which two loci interact within cells. This is achieved by determining the relative abundance of ligation products formed during the 3C protocol that carry sequences from both loci. Individual 3C ligation products that are present in a 3C library, the ChIP-loop library, or the control library can be detected by polymerase chain reaction (PCR) using locus-specific primers. The following protocol outlines the procedure to measure relative abundances of ligation products in these libraries using PCR. The first part of the protocol-library titration-is required only once to determine the linear range of PCR detection. Once the linear range of PCR detection is known for a given ligation product library, follow the second part-interaction analysis-to measure the abundance of ligation products of interest in that library. Specific issues regarding determining the relative abundance of ligation products, designing PCR primers, and quantifying interaction frequencies are also described.</p>
dc.identifier.submissionpathsysbio_pubs/146
dc.contributor.departmentProgram in Systems Biology
dc.contributor.departmentDepartment of Biochemistry and Molecular Pharmacology
dc.source.pagespdb.prot097873


This item appears in the following Collection(s)

Show simple item record