EXPERIMENT_TITLE: GSM4106795: Hi-C: CTCF and STAG2 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 and STAG2 depleted
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "cervical carcinoma"}, {"TAG": "cell type", "VALUE": "HeLa Kyoto"}, {"TAG": "RNAi", "VALUE": "CTCF / STAG2"}, {"TAG": "genotype", "VALUE": "CTCF / STAG2 depleted"}, {"TAG": "chip antibody", "VALUE": "n.a."}]
Pool_Member_@attributes_sample_title: Hi-C: CTCF and STAG2 depleted
RUN_SET_RUN: [{"IDENTIFIERS": {"PRIMARY_ID": "SRR10229705", "SUBMITTER_ID": "GSM4106795_r1"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS5477159", "EXTERNAL_ID": ["SAMN12909708", "GSM4106795"]}, "@attributes": {"member_name": "", "accession": "SRS5477159", "sample_name": "GSM4106795", "sample_title": "Hi-C: CTCF and STAG2 depleted", "spots": "202518989", "bases": "20656936878", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR10229705.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-22/SRR010/229/SRR10229705.sralite.1", "size": "5502951064", "date": "2020-06-20 07:35:28", "md5": "95e2ef69ee5eb650b050e8a534dd4c81", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR10229705", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR10229705/SRR10229705", "size": "8691505876", "date": "2019-10-03 17:51:39", "md5": "fa15e28450d2799f10a56891c7d9357e", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "lane4734_HeLa_SA2_CTCF_NoIndex_L003_R3.fastq.gz", "size": "8364339532", "date": "2019-10-03 17:45:07", "md5": "2e84d5ded181891f814e6ce0d2b48fe8", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "lane4734_HeLa_SA2_CTCF_NoIndex_L003_R1.fastq.gz", "size": "8125144559", "date": "2019-10-03 17:41:39", "md5": "50a6a221a1a72b8597523ca0526c0bb5", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "202518989"}}, "Bases": {"Base": [null, null, null, null, null], "@attributes": {"cs_native": "false", "count": "20656936878"}}, "@attributes": {"alias": "GSM4106795_r1", "accession": "SRR10229705", "total_spots": "202518989", "total_bases": "20656936878", "size": "8691504127", "load_done": "true", "published": "2020-03-19 00:47:54", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR10229706", "SUBMITTER_ID": "GSM4106795_r2"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS5477159", "EXTERNAL_ID": ["SAMN12909708", "GSM4106795"]}, "@attributes": {"member_name": "", "accession": "SRS5477159", "sample_name": "GSM4106795", "sample_title": "Hi-C: CTCF and STAG2 depleted", "spots": "276301529", "bases": "27630152900", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "CAR09ANXX_7_20170302B_20170305_CTCF_SA2_r2.1.fastq.gz", "size": "9843134099", "date": "2019-10-03 20:06:08", "md5": "f4346b4740c08d917a516235d1a67984", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "CAR09ANXX_7_20170302B_20170305_CTCF_SA2_r2.2.fastq.gz", "size": "10141962346", "date": "2019-10-03 20:01:37", "md5": "90d5b8f6c7848853bd267f0335fcb4df", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR10229706.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR010/229/SRR10229706.sralite.1", "size": "7717654576", "date": "2020-06-23 13:43:48", "md5": "49d28e5e7723a5c271725c6198a2d111", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR10229706", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR10229706/SRR10229706", "size": "10583503668", "date": "2019-10-03 20:12:03", "md5": "7faef6983513af125914525d515a3a50", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "276301529"}}, "Databases": {"Database": {"Table": {"Statistics": {"Rows": null, "Elements": null, "@attributes": {"source": "meta"}}, "@attributes": {"name": "SEQUENCE"}}}}, "Bases": {"Base": [null, null, null, null, null], "@attributes": {"cs_native": "false", "count": "27630152900"}}, "@attributes": {"alias": "GSM4106795_r2", "accession": "SRR10229706", "total_spots": "276301529", "total_bases": "27630152900", "size": "10583502136", "load_done": "true", "published": "2020-03-19 00:47:54", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}]