Randomized ligation control for chromosome conformation capture
Program in Systems Biology; Department of Biochemistry and Molecular Pharmacology
Biochemistry, Biophysics, and Structural Biology | Genetics and Genomics | Laboratory and Basic Science Research | Systems Biology
In experiments using chromosome conformation capture followed by PCR (3C-PCR) or chromosome conformation capture carbon copy (5C), it is critical to control for intrinsic biases in the restriction fragments of interest and the probes or primers used for detection. Characteristics such as GC%, annealing temperature, efficiency of 3C primers or 5C probes, and length of restriction fragment can cause variations in primer or probe performance and fragment ligation efficiency. Bias can be measured empirically by production of a random control library, as described here, to be used with the 3C library of interest.
DOI of Published Version
Cold Spring Harb Protoc. 2015 Jun 1;2015(6):587-92. doi: 10.1101/pdb.prot085183. Link to article on publisher's site
Cold Spring Harbor protocols
Belton J, Dekker J. (2015). Randomized ligation control for chromosome conformation capture. Program in Systems Biology Publications. https://doi.org/10.1101/pdb.prot085183. Retrieved from https://escholarship.umassmed.edu/sysbio_pubs/71