Additional data file 4.

(a) Representative agarose gel resolution of amplified multiplex cellular and BAC 5C libraries. Libraries were generated by mixing 29 of each forward and reverse 5C primers with corresponding 3C libraries as described in Materials and methods. BAC 5C library products typically migrate more heterogeneously then cellular counterparts due to increased complexity. (b) Linear schematic representation of HoxA cluster region analyzed in (c). Cluster features are as described in Figure 2b. Predicted BglII restriction pattern below HoxA diagram is shown to scale and restriction fragment number is indicated below each line. Orange shading identifies 'fixed' 3C region and green boxes indicate position of interacting fragments. (c) Detection of individual 5C contacts in multiplex 5C libraries. Formation of four different 5C ligation products in cellular and BAC multiplex 5C libraries was measured with internal 5C primers (right). Interaction frequencies in undifferentiated and differentiated cells were expressed relative to neighboring 71 and 72 interaction, which was set at one. 5C internal priming results are compared to 3C results shown on the left. 3C data are from Figures 3 &4 except that interaction frequencies were expressed relative to contact neighboring fixed region as described above. Each histogram value represents the average of at least three PCR reactions and error bars correspond to standard error of the mean. 5C internal primer sequences are shown in Additional data file 4.

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Fraser et al. Genome Biology 2009 10:R37   doi:10.1186/gb-2009-10-4-r37