Materials
Name | Company | Catalog Number | Comments |
RPMI1640 medium | Invitrogen | 22400-105 | |
acrylamide | Invitrogen | 15512-023 | |
ATP solution, 10mM | Invitrogen | AM8110G | |
fetal bovine serum | Invitrogen | 16000-044 | |
penicillin-streptomycin | Invitrogen | 15140-122 | |
1M Tris pH8.0 | Invitrogen | AM9856 | |
RNase A | Invitrogen | 12091-039 | |
SDS | Invitrogen | 15525-017 | |
urea | Invitrogen | 15505-035 | |
BamH I | New England Biolabs | R0136T | |
Bgl II | New England Biolabs | R0144M | |
Dpn II | New England Biolabs | R0543T | |
Msp I | New England Biolabs | R0106S | |
dNTPs | New England Biolabs | N0447L | |
proteinase K | New England Biolabs | P8102S | |
T4 DNA ligase | New England Biolabs | M0202T | |
37% formaldehyde | Sigma-Aldrich | F8775 | |
Bis-acrylamide | Sigma-Aldrich | 146072 | |
dithiothreitol | Sigma-Aldrich | 43815 | |
glycine | Sigma-Aldrich | 50046 | |
PMSF | Sigma-Aldrich | 93482 | |
proteinase inhibitor | Sigma-Aldrich | S8830 | |
Nonidet P-40 | Roche Group | 11754599001 | |
KlenTaq1 | Ab peptides | 1001 | |
dCTP alpha P32 | PerkinElmer, Inc. | BLU513H250UC | |
PTC-100 Thermal Cycler | MJ Research | mjptc100 | |
Power Supply | Bio-Rad | 164-5056 | |
OmniPAGE Maxi | Aurogene Life Science | VS20D | |
Typhoon 9400 | GE Healthcare | 63-0055-78 |
References
- Dekker, J., Rippe, K., Dekker, M., Kleckner, N. Capturing chromosome conformation. Science. 295, 1306-1311 (2002).
- Apostolou, E., Thanos, D. Virus Infection Induces NF-kappaB-dependent interchromosomal associations mediating monoallelic IFN-beta gene expression. Cell. 134, 85-96 (2008).
- Duan, Z. A three-dimensional model of the yeast genome. Nature. 465, 363-367 (2010).
- Lomvardas, S. Interchromosomal interactions and olfactory receptor choice. Cell. 126, 403-413 (2006).
- Murrell, A., Heeson, S., Reik, W. Interaction between differentially methylated regions partitions the imprinted genes Igf2 and H19 into parent-specific chromatin loops. Nat Genet. 36, 889-893 (2004).
- Schoenfelder, S. Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells. Nat Genet. 42, 53-61 (2010).
- Spilianakis, C. G., Lalioti, M. D., Town, T., Lee, G. R., Flavell, R. A. Interchromosomal associations between alternatively expressed loci. Nature. 435, 637-645 (2005).
- Vakoc, C. R. Proximity among distant regulatory elements at the beta-globin locus requires GATA-1 and FOG-1. Mol Cell. 17, 453-462 (2005).
- Xu, N., Tsai, C. L., Lee, J. T. Transient homologous chromosome pairing marks the onset of X inactivation. Science. 311, 1149-1152 (2006).
- Lieberman-Aiden, E. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 326, 289-293 (2009).
- Berkum, N. L. van Hi-C: a method to study the three-dimensional architecture of genomes. J Vis Exp. , (2010).
- Ling, J. Q. CTCF mediates interchromosomal colocalization between Igf2/H19 and Wsb1/Nf1. Science. 312, 269-272 (2006).
- Dekker, J. The three 'C's of chromosome conformation capture: controls, controls, controls. Nat Methods. 3, 17-21 (2006).