EXPERIMENT_TITLE: GSM4831164: Thp1-mono-sciDLOHiC; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: DNA was precipitated at room temperature with 10 µl of Dr. GenTLE Precipitation Carrier (Takara), 100 µl of 3M sodium acetate (pH 5.2), and an equal volume of isopropanol. For sciDLO Hi-C library construction, the cells were firstly pooled for fixation, in situ digestion and then aliquoted to 96 wells to added the first barcode through ligation of barcoded MmeI half linker. The intact nucleus was pooled again for proximity ligation and then aliquoted to about 30 nucleus per tube for multiple displacement amplification (MDA). The amplification products were digested by MmeI digestion which released a specific 80-bp barcoded chromatin interaction DNA fragment. As we only recycled these DNA fragments containing chromatin interaction pairs, it can greatly reduce the sequencing noise caused by MDA, which is an advantage of this method. Moreover, the number of barcode indexes (96) in each tube exceeds the number of nuclei (30), the vast majority of single nuclei are tagged by a unique barcode.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Next-generation sequencing data of single cell indexed DLO Hi-C library of Thp1-mono, Thp1-macro, and Thp1-M.tb. Overall design: We constructed in situ DLO Hi-C library of 3 samples (Thp1-mono, Thp1-macro, and Thp1-M.tb), and for each sample we did 14 sub-library.
SAMPLE_TITLE: Thp1-mono-sciDLOHiC
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "Peripheral blood"}, {"TAG": "cell line", "VALUE": "THP-1"}, {"TAG": "treatment", "VALUE": "Before differentiation"}]
Pool_Member_@attributes_sample_title: Thp1-mono-sciDLOHiC
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