EXPERIMENT_TITLE: GSM4911599: iHiC2_CM; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Standard DNA isolation Hi-C performed for mESC according to the iHi-C published protocol DOI:10.15252/msb.20167311 and for hiPSC-CM according to the modified iHi-C 2.0 protocol DOI: 10.1016/j.ymeth.2019.07.003
STUDY_DESCRIPTOR_STUDY_ABSTRACT: The advent of the chromosome conformation capture (3C) and related technologies has profoundly renewed our understaning of three-dimensional chromatin folding in mammalian nuclei. Alongside these experimental approaches, numerous computational tools for handling, normalizing, visualizing, and ultimately detecting interactions in 3C-type datasets are being developed. Here, we present Bloom, a comprehensive method for the analysis of 3C-type data matrices on the basis of Dirichlet process mixture models that addresses two important open issues. First, it retrieves occult interaction patterns from sparse data, like those derived from single-cell or “native” Hi-C experiments; thus, bloomed sparse data can now be used to study interaction landscapes at high-resolution. Second, it detects enhancer-promoter interactions with high sensitivity and inherently assigns an interaction frequency score (IFS) to each contact. Using enhancer perturbation data of different throughput, we show that IFS accurately quantifies the regulatory influence of each enhancer on its target promoter. As a result, Bloom allows decoding of complex regulatory landscapes by generating functionally-relevant enhancer atlases solely on the basis of 3C-type data. Overall design: HiC experiments on 5x106 mESC and 106 CM cells.
SAMPLE_TITLE: iHiC2_CM
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "iPS-derived cardiomyocytes cells (hIPSC-CM)"}, {"TAG": "cell type", "VALUE": "human induced pluripotent stem cell-derived cardiomyocytes"}, {"TAG": "genotype", "VALUE": "wt"}, {"TAG": "library id", "VALUE": "75726"}]
Pool_Member_@attributes_sample_title: iHiC2_CM
RUN_SET_RUN_Pool_Member_@attributes_sample_title: iHiC2_CM
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