EXPERIMENT_TITLE: GSM8501039: Hap1, 10000 cells, Hi-C; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Hi-C libraries were prepared using FLIE Hi-C protocol. Cells were crosslinked with 2% formaldehyde. The cells were lysed in cold lysis buffer (10 mM Tris-HCl, pH 8.0, 10 mM NaCl, 0.2% Igepal CA-630) to permeabilize the nuclei. The nuclei were digested with DpnII restriction enzyme, following by end-filling with biotin-14-dATP, dCTP, dGTP, and dTTP with Klenow. Blunt ends were ligated with T4 DNA ligase, and the formaldehyde crosslinking was reversed by proteinase K (10 mg/ml). DNA was purified using phenol-chloroform and ethanol precipitation, sonicated to an average size of 200 bp, and biotin was removed from non-ligated DNA ends with T4 polymerase. Biotinylated chimeric DNA strands were pulled down using streptavidin beads (Dynabeads C1). Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina according to the manufacturer's instructions.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: We developed FLIE (Fast Low-Input Efficient) Hi-C, a highly optimized and simplified version of Hi-C. Our method shortens the duration of Hi-C from five days to two days and decreases key reagent amounts 5-20 fold, while maintaining experimental controls and data quality. Importantly, the method also reduces the required input material by 100-1000 fold, as we demonstrate by generating detailed high complexity interaction maps from low-input sorted mouse frozen neuron nuclei and from 5,000-10,000 human Hap1 cells. Overall design: FLIE Hi-C (optimized Hi-C protocol) on Hap1 cells and frozen mouse neuron nuclei
SAMPLE_TITLE: Hap1, 10000 cells, Hi-C
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "Hap1"}, {"TAG": "cell line", "VALUE": "Hap1"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
Pool_Member_@attributes_sample_title: Hap1, 10000 cells, Hi-C
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