Illumina Genome Analyzer II paired end sequencing; Metaphase-Chromosome-Organization
Metaphase-Chromosome-Organization
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). 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) Hi-C was performed following (Lieberman and van Berkum et al., Science, 2009) with modifications detailed in (Naumova et al., 2013).
Experimental Factor: cell cycle stage
G1mid