EXPERIMENT_TITLE: GSM7682321: GM12878_cell_051_HiC; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Viable cells were picked into a single tube containing 7 μL soft cell lysis buffer (25 mM Tris pH8.3, 30 mM NaCl, 0.45% IGEPAL-CA630, 1 U/μL SUPERaseIn) supplemented with 0.25 μL magnetic beads, then incubate on ice for 30 min, after incubation, vortex for 1 min. Centrifuge at 500 x g for 5 min at 4°C, then take 5 μL supernatant to a new tube. The supernatant was proceeded to Smart-seq2 reverse transcription and amplification5. Nuclei was proceeded to chromosome conformation capture. simultaneous 3D genome and gene expression by LiMCA Smart-seq2 for LiMCA RNA library; Dip-C protocol for LiMCA Hi-C library
STUDY_DESCRIPTOR_STUDY_ABSTRACT: The simultaneous measurement of three-dimensional (3D) genome structure and gene expression of individual cells is critical for understanding our genome's structure–function relation, yet is extremely challenging for existing methods. Here we present Linking mRNA to Chromatin Architecture (LiMCA), which jointly profiles 3D genome and transcriptome with exceptional sensitivity and from low-input materials. Combining LiMCA and our high-resolution scATAC-seq assay, METATAC, we profiled the developing mouse olfactory epithelium and reported the first chromatin accessibility profiles and the first paired 3D genome structures and gene expression information of single neurons. We greatly expanded the repertoire of known OR enhancers, and discovered unexpected rules of their dynamics: ORs and their enhancers are most accessible during early differentiation, and the active OR typically does not associate with the largest enhancer hub. These findings offer valuable insights into how 3D connectivity of ORs and enhancers dynamically orchestrate the “one neuron–one receptor” selection process. Overall design: 10X Genomics scRNA-seq and METATAC scATAC-seq for mouse olfactory epithelium
SAMPLE_TITLE: GM12878_cell_051_HiC
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "blood"}, {"TAG": "tissue", "VALUE": "blood"}, {"TAG": "cell line", "VALUE": "Lymphoblastoid"}, {"TAG": "cell type", "VALUE": "GM12878"}, {"TAG": "genotype", "VALUE": "WT"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
Pool_Member_@attributes_sample_title: GM12878_cell_051_HiC
RUN_SET_RUN_Pool_Member_@attributes_sample_title: GM12878_cell_051_HiC
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