EXPERIMENT_TITLE: GSM4106794: Hi-C: CTCF depleted; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: ChIP-Seq: Cells were cross-linked and scrapped of the plate. The DNA was fragmented and the protein of interest was immunoprecipitated with indicated antibodies; Adaptors were ligated to the 5' and 3' ends and the library was prepared for Illumina sequencing by a qPCR amplification step. ChIP as well as Hi-C libraries were prepared for sequencing using standard Illumina protocols.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: The human genome folds to create thousands of loops connecting sites that are bound by the insulator protein CTCF and the ring-shaped cohesin complex. It is thought that most of these loops emerge through a process whereby cohesin extrudes chromatin, forming an initially small loop that grows larger and larger until the loop's expansion is arrested by CTCF. Cohesin rings comprise four proteins: SMC1, SMC3, SCC1, and, in higher eukaryotes, either STAG1 or STAG2. We explore differential roles of especially STAG1, STAG2 and ESCO1 proteins in chromatin organization. Overall design: We combine Hi-C and ChIP-Seq data with FRAP and physical simulations to dissect the roles of these two forms of cohesin - STAG1 and STAG2 - in G1 phase.
SAMPLE_TITLE: Hi-C: CTCF depleted
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "cervical carcinoma"}, {"TAG": "cell type", "VALUE": "HeLa Kyoto"}, {"TAG": "RNAi", "VALUE": "CTCF"}, {"TAG": "genotype", "VALUE": "CTCF depleted"}, {"TAG": "chip antibody", "VALUE": "n.a."}]
Pool_Member_@attributes_sample_title: Hi-C: CTCF depleted
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