Quantitative analysis of chromosome conformation capture assays (3C-qPCR)

By H. Hagège, P. Klous, C. Braem, Erik Splinter, Job Dekker, G. Cathala, W. de Laat, T. Forné. Nature Protocols, 2007

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Androgen Receptor Regulates a Distinct Transcription Program in Androgen-Independent Prostate Cancer (2009, methodology): “3C-qPCR assays were performed essentially as described (Hagege et al., 2007) with minor modifications.”
Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture (2011, methodology): “The inherent throughput limitations of the traditional visual methods for quantifying chromosomal structure have been alleviated over the last few years with the development of the chromosome conformation capture (3C) technique for quantifying contact probabilities between specific loc”
A decade of 3C technologies: insights into nuclear organization. (2012, background): “For this and other reasons, (semi)quantitative 3C PCR is notoriously difficult and requires strict controls and careful experimental design and data interpretation (Dekker 2006; Hagege et al. 2007; Simonis et al. 2007).”