EXPERIMENT_TITLE: GSM8688950: Human PGCLC generated from hiPSC-A4, Hi-C seq; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Cell cultures were exposed to formaldehyde for proximal ligation and lysed following the protocol of Arima Genomics Hi-C kit (Cat# A510008). Illumina compatible Hi-C libraries were prepared using Arima Genomics Hi-C kit (Cat# A510008).
STUDY_DESCRIPTOR_STUDY_ABSTRACT: The pluripotent stem cell (PSC)-derived human primordial germ cell-like cells (PGCLCs) are a cell culture-derived surrogate model of embryonic primordial germ cells. Upon differentiation of PSCs to PGCLCs, multiple loci of HML-2, the hominoid-specific human endogenous retrovirus (HERV), are strongly activated, which is necessary for PSC differentiation to PGCLCs. In PSCs, strongly ac-tivated loci of HERV-H family HERVs create chromatin contacts, which are required for the plu-ripotency. Chromatin contacts in the genome of human PSCs and PGCLCs were determined by Hi-C sequencing, and their locations were compared with those of HML-2 loci strongly activated in PGCLCs but silenced in the precursor naïve iPSCs. In both iPSCs and PGCLCs, the size of chromatin contacts were found to be around one megabase, which corresponds to the Topologically Associ-ated Domains in the human genome but is slightly larger in PGCLCs than iPSCs. The number of small-sized chromatin contacts diminished while numbers of larger-sized contacts increased. The distances between chromatin contacts newly formed in PGCLCs and the degrees of activation of the closest HML-2 loci showed significant inverse correlation. Our study provides evidence that strong activation of HML-2 provirus loci may be associated with newly formed chromatin contacts in their vicinity, potentially contributing to PSC differentiation to the germ cell lineage. Overall design: Hi-C sequencing of proximally ligated DNA isolated from human naïve iPSCs and PGCLCs
SAMPLE_TITLE: Human PGCLC generated from hiPSC-A4, Hi-C seq
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "A4"}, {"TAG": "cell line", "VALUE": "A4"}, {"TAG": "cell type", "VALUE": "PGCLC culture"}, {"TAG": "Sex", "VALUE": "male"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
Pool_Member_@attributes_sample_title: Human PGCLC generated from hiPSC-A4, Hi-C seq
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Human PGCLC generated from hiPSC-A4, Hi-C seq
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