title: HL60_d2
organism: Homo sapiens
description: Protocols: HL60-cells were treated with ATRA for 2 and 5 days, and harvested for Hi-C study. 2×10^7 Cells were fixed by 1% formaldehyde (v/v) for 15 min at room temperature (RT) with slowly rotation. Cells were lysed by 550 μl lysis buffer (500 μl 10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% Igepal CA-630 and 50 μl protease inhibitors) using a homogenizer, and harvested the chromatin at 5,000 rpm and washed twice. The pellet was added 1% SDS and incubated at 65 oC for 10 min, then quenched by Triton X-100. The chromatin was digested by 600 U MboI (NEB, Ipswich, USA) at 37 oC overnight. For 3C, HindIII and KpnI were used to digeste the chromatin. The next day, enzymes were inactivated by 10% SDS at 65 oC for 30 min, and the restriction fragment overhangs were filled in using biotin-14-dCTP and Klenow at 37 oC for 45 min, and the ligation was conducted in 7.61 ml ligation mix (745 μl 10% Triton X-100, 745 μl 10x ligation buffer (500 mM Tris-HCl pH 7.5, 100 mM MgCl2, 100 mM DTT), 80 μl 10 mg/ml BSA, 80 μl 100 mM ATP and 5.96 ml water) for 4 h at 16°C. The blunt-end Hi-C ligation was sonicated and pull down by streptavidin beads, then purified by ethanol. Hi-C library was prepared for paired ending sequencing using NEBNext® UltraTM DNA Library Prep Kit for Illuina® (NEB).
attributes.tag: ENA-FIRST-PUBLIC
attributes.value: 2020-05-07T17:05:44Z
attributes.tag: ENA-LAST-UPDATE
attributes.value: 2019-11-25T14:21:51Z
attributes.tag: External Id
attributes.value: SAMEA6245497
attributes.tag: INSDC center name
attributes.value: The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan 450008, PR. China
attributes.tag: INSDC first public
attributes.value: 2020-05-07T17:05:44Z
attributes.tag: INSDC last update
attributes.value: 2019-11-25T14:21:51Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-8547:HL60_d2
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: cell line
attributes.value: HL-60
attributes.tag: cell type
attributes.value: leukocyte
attributes.tag: common name
attributes.value: human
attributes.tag: developmental stage
attributes.value: adult
attributes.tag: disease
attributes.value: acute promyelocytic leukemia
attributes.tag: genotype
attributes.value: wild type genotype
attributes.tag: organism part
attributes.value: blood
attributes.tag: sample name
attributes.value: E-MTAB-8547:HL60_d2
attributes.tag: scientific_name
attributes.value: Homo sapiens