7 protocols
AccessionNameType
 
normalization data transformation protocol
Reads were aligned to hg19 using novoalign as described in (Sanyal et al., Nature, 2012)
 
normalization data transformation protocol
Reads were aligned to hg19 using Bowtie2 as described in (Imakaev and Fudenberg et al., Nature Methods, 2012)
 
nucleic acid sequencing protocol
Libraries were sequenced on the Illumina GAIIx and HiSeq2000 paired end sequencing platform at the University of Massachusetts Medical School deep sequencing core facility (Nemo).
 
growth protocol
HeLa cells were grown in standard DMEM media with sodium pyruvate (Gibco #11995073) with 10 % Bovine serum (Gibco #16170078), 1% PenStrep (Gibco #15140) and 1% Antibiotic-Antimycotic agent (Gibco # 15240). HFF cells were grown in standard DMEM media with sodium pyruvate (Gibco #11995073) with 10 % FBS (BenchMark #100-101), 1% PenStrep (Gibco #15140) and 1% Antibiotic-Antimycotic agent (Gibco # 15240). K562 cells were maintained in standard RPMI-1640 media with 2 mM L-glutamine (Gibco #22400-089) with 10% FBS (BenchMark #100-101), 1% PenStrep (Gibco #15140) and 1% Antibiotic-Antimycotic agent (Gibco # 15240).
 
nucleic acid library construction protocol
5C was performed following (Dostie, Genome Reserach, 2006), as detailed in (Naumova et al., 2013).
 
Cell synchronization
To collect HeLs cells arrested in S-phase, cells were synchronized by double Thymidine block (2mM thymidine in grouth media). HeLa cells in G1 phase were obtained by double thymidine block followed by release into normal growth media for 12h (early G1) or 14h (middle G1). To collect mitotic cells, HeLa, HFF-1 and K562 cells were synchronized by double Thymidine block followed by release into normal growth media for several hous. Then cells were arrested in Metaphase by adding nocodazole at 100ng/mkl final concentration in grouth medai as described in (Naumova et al. 2013)
 
nucleic acid library construction protocol
Hi-C was performed following (Lieberman and van Berkum et al., Science, 2009) with modifications detailed in (Naumova et al., 2013).