EXPERIMENT_TITLE: GSM7869401: iPSC_S1Hi-C; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Extraction protocol was performed as described in (Gridina. et. al 2021). Library construction protocol similar to the performed as described in (Gridina. et. al 2021) with some adaptions (see the paper for detailed protocol)
STUDY_DESCRIPTOR_STUDY_ABSTRACT: This study presents a novel approach for mapping global chromatin interactions using S1 nuclease, a sequence-agnostic enzyme. We develop and outline a protocol that leverages S1 nuclease's ability to effectively introduce breaks into both open and closed chromatin regions, allowing for comprehensive profiling of chromatin properties. Our S1 Hi-C method enables the preparation of high-quality Hi-C libraries, marking a significant advancement over previously established DNase I Hi-C protocols. Moreover, S1 nuclease's capability to fragment chromatin to mono-nucleosomes suggests the potential for mapping the three-dimensional organization of the genome at high resolution. This methodology holds promise for an improved understanding of chromatin state-dependent activities and may facilitate the development of new genomic methods. Overall design: Human K562 cells were grown in RPMI-1640 medium with 10% FBS and a penicillin/streptomycin mix. Human peripheral blood mononuclear cells (PBMC) were isolated from peripheral blood samples, which were collected in tubes with EDTA. RBC lysis buffer (BioLegend) was used for erythrocyte removal according to the manufacturer's instructions. Isolated PBMCs were processed immediately for crosslinking. We then obtained the Hi-C libraries following our own protocol. *** Raw data not provided for the patient samples (PBMC) due to privacy concerns. ***
SAMPLE_TITLE: iPSC_S1Hi-C
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "induced pluripotent stem cells"}, {"TAG": "cell type", "VALUE": "induced pluripotent stem cells"}, {"TAG": "cell line", "VALUE": "iPSC"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
Pool_Member_@attributes_sample_title: iPSC_S1Hi-C
RUN_SET_RUN_Pool_Member_@attributes_sample_title: iPSC_S1Hi-C
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