EXPERIMENT_TITLE: GSM6617841: RPE-DMSO; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: cells were washed twice with PBS and digested with Trypsin–EDTA 0.05% (Gibco) for 10 min at 37 °C. A 40-µm cell strainer was used to obtain single cells. The cell suspension was pelleted at 300g for 5 min and resuspended with cold 10% FCS. Subsequently, the cells were fixed by adding an equal volume of 4% formaldehyde (Sigma-Aldrich). The suspension was mixed for 10 min while shaking at room temperature in 50 ml tubes. Exactly after 10 min the fixation was quenched with 500 µl 1.425 M glycine (Merck) on ice. The suspension was pelleted at 400g for 8 min and resuspended in cold lysis buffer (50 mM Tris, pH 7.5; 150 mM NaCl; 5 mM EDTA; 0.5% NP-40; 1.15% Triton X-100; protease inhibitors (Roche)). Next we followed Hi-C protocol. Universal sequencing adaptor were added using the NEBnext Ultra DNA Library Kit (NEB) according to the supplier's recommendation. The PCR cycle number was adjusted to 4–12 based on the initial DNA concentration. The final libraries were purified using AMPure Beads (Beckman Coulter) and samples were sequenced with Ilumina Hi-Seq technology according to the standard protocols.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: To investigate the function of TOP2 on chromatin structure of human cells, we performed Hi-C using chromatin obtained from RPE1 cells. Overall design: Pairwise comparison of the Hi-C maps of four different conditions: 1) control (DMSO-treatment), 2) treated with ICRF193  in final concentration 5uM or treated with doxorubicin in final concentration 3) 200 nM and 4) 340 nM.
SAMPLE_TITLE: RPE-DMSO
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "RPE1"}, {"TAG": "cell line", "VALUE": "RPE1"}, {"TAG": "cell type", "VALUE": "Human retinal pigment epithelial"}, {"TAG": "genotype", "VALUE": "WT"}, {"TAG": "treatment", "VALUE": "DMSO"}, {"TAG": "time", "VALUE": "18 h"}]
Pool_Member_@attributes_sample_title: RPE-DMSO
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