EXPERIMENT_TITLE: GSM8698727: GM12878 and mESC cell mixture, dscHi-C, cultured; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Cultured cell line or isolated nuclei from primary brain cortex were processed with Hi-C 3.0 protocol. Cells were firstly double-crosslinked with PFA followed by DSG, then treated with SDS and Triton X-100 to open chromatin. Then the chromatin was digested by resuspending the nuclei in digestion mix containing DdeI and DpnII without detergent, and incubated at 37°C for 2 hours, followed by inactivating the REs. The DNA ends was filled by biotin labeled dATP, followed by proximity ligation using T4 ligase by incubating at room temperature for 2 hours. For sample prepared for dscHi-C multiome experiment, all reaction mix was supplemented 0.5 U/μL Protector RNase inhibitor. Nuclei processed through Hi-C 3.0 procedure were bulk tagmented with Tn5 transposome, then loaded to 10x Chromium platform according to either ATAC kit or multiome kit. For dscHi-C, the DNA were barcoded by linear amplification in droplet, followed pooling droplets, further amplification and sample index were incorporated. For dscHi-C-multiome, the DNA and RNA from the same cell were barcoded in droplet, the then droplets were pooled and nuclei were decrosslinked. Genomic DNA were pull down using streptavidin beads, and cDNA were further proceeded with second time reverse transcription. Then the genomic DNA were direct subjected to library preparation. The cDNA were further fragmented and amplified for library construction.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Single-cell three-dimensional (3D) genome techniques have advanced our understanding of cell-type-specific chromatin structures in complex tissues, yet current methodologies are limited in cell throughput. Here we introduce a high-throughput single-cell Hi-C approach (dscHi-C) and its transcriptome co-assay (dscHi-C-multiome) using droplet microfluidics. Using dicHi-C, we investigated chromatin structural changes during mouse brain aging by profiling 32,777 single cells across three developmental stages (3 month, 12 month and 23 month), yielding a median of 78,220 unique contacts. Our results show that genes with significant structural changes are enriched in pathways related to metabolic process and morphology change in neurons, and innate immune response in glial cells, highlighting the role of 3D genome organization in physiological brain ageing. Furthermore, our multi-omics joint assay, dscHi-C-multiome, enables precise cell type identification in the adult mouse brain and uncovers the intricate relationship between genome architecture and gene expression. Collectively, we developed the sensitive, high-throughput dscHi-C and its multi-omics derivative, dscHi-C-multiome, demonstrating their potential for large-scale cell atlas studies in development and disease. Overall design: In this study, we performed droplet-based single-cell Hi-C (dscHi-C) and its transcriptome co-assay (dscHi-C-multiome) on human and mouse cell line, and mouse brain cortex tissues.
SAMPLE_TITLE: GM12878 and mESC cell mixture, dscHi-C, cultured
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "B lymphoblastoid, mouse embryonic stem cell"}, {"TAG": "cell line", "VALUE": "B lymphoblastoid, mouse embryonic stem cell"}, {"TAG": "cell type", "VALUE": "B lymphoblastoid, mouse embryonic stem cell"}, {"TAG": "genotype", "VALUE": "WT"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
Pool_Member_@attributes_sample_title: GM12878 and mESC cell mixture, dscHi-C, cultured
RUN_SET_RUN_Pool_Member_@attributes_sample_title: GM12878 and mESC cell mixture, dscHi-C, cultured
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