GSM4212835: HiC_Pfhmgb1_RC_rep1; Plasmodium falciparum; Hi-C
Parasites were lysed in 5 ml ice-cold lysis buffer with rotation for 1 h at 4 °C and washed twice with PBS and once with 1×NEBuffer 2. Pelleted nuclei was resuspended with 300 μl H2O, 44 μl of 10×NEBuffer 2 and  38 μl of 1% SDS at 65 °C water bath 10 minutes and reaction was terminated by addition of T44 μl of 10% Triton X-100. To fragment DNA, 350 U endonucleases DpnII (NEB,R0543M) was added to the reaction at 37 °C overnight. Digested DNA was filled in the restriction fragment overhangs with Klenow (NEB,M0210L) and marked the DNA ends with biotin. Chromatin was then ligated with T4 DNA ligase(NEB) for 4 h at 16 °C, reversed with proteinase K and purified with  phenol:chloroform and ethanol protocol. After removal of biotin from un-ligated ends with T4 DNA polymerase (NEB,  M0203L), DNA was sonicated to reduce their size to 300-500 bp. To prepare biotinylated DNA, sheared DNA were immobilized on Dynabeads M-280 Streptavidin at room temperature for 1 h with rotation. The process of ends repair, A-tailing and adaptor ligation referring to ChIP library, the Hi-C library was amplified 6-10 cycles and the PCR product was loaded to 2% agarose and size selected 300-600bp band. The library were sequenced on an Illumina HiSeq Xten systerm with PE150 strategy.
GEO Accession
GSM4212835