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. Author manuscript; available in PMC: 2018 Jan 11.
Published in final edited form as: Nat Rev Mol Cell Biol. 2016 Sep 1;17(12):743–755. doi: 10.1038/nrm.2016.104

Table 2.

Design and implementation of Capture-HiC experiments

Oligo array vendor Probe Organism Target (or targets) Control (or controls) Hi-C library protocol Refs
Agilent SureSelect RNA Human Breast cancer risk loci Size-matched gene dessert regions Hind III dilution Hi-C 58
Agilent SureSelect RNA Human Colon cancer risk loci N/A Hind III dilution Hi-C 59
In-house* RNA Human MHC and KIR loci N/A Hind III dilution Hi-C 29
In-house* RNA Human Three ~2-Mb loci N/A Mbo I in situ Hi-C 60
Roche Nimblegen SeqCap DNA Human LncRNA promoters β-Globin LCR, NANOG, and SOX2 loci DNase I dilution Hi-C 49
Agilent SureSelect RNA Mouse Promoters Random ligation library‡ Hind III dilution Hi-C 56
Agilent SureSelect RNA Mouse Promoters Random ligation library‡ Hind III Dilution Hi-C 57
Agilent SureSelect RNA Human Promoters Random ligation library‡ Hind III Dilution Hi-C 54
Agilent SureSelect RNA Human Promoters and autoimmune disease risk loci HBA locus Hind III dilution Hi-C 53
Roche Nimblegen SeqCap DNA Mouse Promoters Intergenic and exonic regions Mbo I dilution Hi-C 55

HBA, haemoglobin subunit alpha; LCR, locus control region; LncRNA, long non-coding RNA; N/A, not applicable.

*

Single-strand DNA oligonucleotides are obtained from CustomArray and synthesized into RNA probes in-house.

‡

In the random ligation library, crosslinks are reversed before the proximity ligation reaction.