Extended Data Fig. 3: In vitro and in silico Hi-C experiments show that OR Hi-C contacts are generated by unique sequences that do not map to other OR clusters.

a, Contact matrices from in vitro Hi-C (top) using a 165-kb BAC plasmid containing seven OR genes from an OR cluster from chromosome 1 and in situ Hi-C from mOSNs (bottom). Hi-C contacts in the BAC Hi-C are restricted to the coordinates of the BAC plasmid and do not extend to two OR genes from this cluster that are absent from the BAC. b, Virtual 4C from the 165-kb BAC region to chromosome 2, which contains the highest number of OR genes. Top, virtual 4C from the BAC in vitro Hi-C shows that no reads mapped to ORs from chromosome 2, whereas the same 165-kb regions makes abundant trans contacts with these ORs in mOSNs. c, Of all the BAC Hi-C contacts, 99.3% map within the BAC, whereas in mOSNs only 21.7% of the BAC region Hi-C contacts map within the BAC. d, In silico Hi-C analysis shows complete absence of mis-mapped reads corresponding to OR clusters under the mapping conditions used throughout the manuscript (removing mapq < 30). Each OR cluster was subjected to intracluster in silico Hi-C (g) and then the Hi-C contacts of the 69 OR clusters were mapped in aggregate to the whole genome. As seen in the contact matrix from chromosomes 2 and 9 (d), the in silico reads only map within clusters, with no mis-mapped reads that would erroneously be interpreted as intercluster cis or trans contacts. e, For reference, the corresponding in situ Hi-C from mOSNs. f, Aggregate analysis for all 69 OR gene clusters shows that our mapping protocol does not mis-map any Hi-C contacts to the wrong OR cluster. g, Brief description of the pipeline used for the in silico analysis.