EXPERIMENT_TITLE: GSM7759627: HiC hPSC shLUC Repeat 2; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: The cell was digested into single cell with accutase. Cell was washed three times with DPBS and crosslinked with 1% formaldehyde for 10 min at room temperature. The chromatin was digested with HindIII restriction enzyme, the biotinylated dATP was ligated in to the overhang site which generated by HindIII digestion. After reversal of crosslinks, the genome DNA was purified and sheared, the fragment was select around 300-500bp, the point ligation junctions with biotinylated dATP were pulled down with streptavidin beads and prepped for Illumina sequencing. Libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina
STUDY_DESCRIPTOR_STUDY_ABSTRACT: During early embryogenesis the fertilized zygote proceeds through an intricate developmental program, accompanyed by DNA and chromatin remodelling. However, the mechanisms governing this reconfiguring are poorly understood. Parts of the embryogenesis developmental program can be captured in vitro in the form of two types of human pluripotent stem cells (hPSC): naïve and primed hPSCs. Naïve hPSCs resemble the inner cell mass of the blastocyst, whilst primed hPSCs resemble the post-implantation embryo. The nucleus is made of DNA wrapped around chromatin, and the nuclear matrix, a proteinaceous gel that provides  structure. Here, we show that disruptions in the nuclear matrix caused primed hPSCs to spontaneously convert to the naïve, earlier embryonic state. Overall design: Hi-C was performed in hPSCs (H1 line) in cells transfected with an shRNA targetting Luciferase (LUC) as a control, or against (HNRNPU)
SAMPLE_TITLE: HiC hPSC shLUC Repeat 2
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "cell line"}, {"TAG": "tissue", "VALUE": "cell line"}, {"TAG": "cell line", "VALUE": "hPSCs H1"}, {"TAG": "cell type", "VALUE": "Pluripotent Stem Cells"}, {"TAG": "shRNA", "VALUE": "shRNA targetting LUC"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
Pool_Member_@attributes_sample_title: HiC hPSC shLUC Repeat 2
RUN_SET_RUN_Pool_Member_@attributes_sample_title: HiC hPSC shLUC Repeat 2
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR25917782.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-zq-20/SRR025/25917/SRR25917782/SRR25917782.lite.1", "size": "37730726391", "date": "2023-09-10 19:54:01", "md5": "2204139bc7928b6a0db9efddf648332f", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR25917782", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR25917782/SRR25917782", "size": "50103701995", "date": "2023-09-05 18:58:09", "md5": "44f50317cdc054c752407d5f974257b0", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Hs_hpsc_shLUC.rp2.p2.fq.gz", "size": "36293864378", "date": "2023-09-05 18:50:12", "md5": "63e4526586775a4b00c94e94c2e829ed", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Hs_hpsc_shLUC.rp2.p1.fq.gz", "size": "34376173246", "date": "2023-09-05 18:48:30", "md5": "59ad6d1f1cbf1b1ffe7149f13d2299e7", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]