EXPERIMENT_TITLE: GSM5538494: H9 hESC shLuc; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Human embryonic cells were washed with PBS and fixed with 2% formaldehyde for 10min at RT. Hi-C samples were prepared with the Arima Hi-C Kit, and libraries were preapred with the KAPA HyperPrep Kits following the manufacturer's instructions
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Pluripotent stem cells are unique in their large nucleus and manifestly open chromatin structure with hypertranscriptional activities. How the nucleolus, the largest membraneless and phase-separated subnuclear organelle, maintains its structural integrity in pluripotency maintenance remains incompletely understood. By studying nucleolus-specific DEAD-box RNA helicase-18 (DDX18) in human embryonic stem cells, we discover mechanisms controlling nucleolus phase separation and chromatin organization. Overall design: In this experiment, we characterized hESCchromatin interaction under control and DDX18 knockdown condition using  Hi-C seq.
SAMPLE_TITLE: H9 hESC shLuc
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "H9 hESC shLuc"}, {"TAG": "cell types", "VALUE": "human ESC"}, {"TAG": "strain", "VALUE": "H9"}, {"TAG": "tatreatment", "VALUE": "shLuc"}]
Pool_Member_@attributes_sample_title: H9 hESC shLuc
RUN_SET_RUN: [{"IDENTIFIERS": {"PRIMARY_ID": "SRR15624025", "SUBMITTER_ID": "GSM5538494_r1"}, "EXPERIMENT_REF": null, "RUN_ATTRIBUTES": {"RUN_ATTRIBUTE": {"TAG": "loader", "VALUE": "fastq-load.py", "UNITS": null}}, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS9931916", "EXTERNAL_ID": ["SAMN20994885", "GSM5538494"]}, "@attributes": {"member_name": "", "accession": "SRS9931916", "sample_name": "GSM5538494", "sample_title": "H9 hESC shLuc", "spots": "87925310", "bases": "8968381620", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR15624025.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos6/sra-pub-zq-40/SRR015/15624/SRR15624025/SRR15624025.lite.1", "size": "2343476176", "date": "2023-02-06 14:19:28", "md5": "4528ea519a5762d0156ccf16ea9a238f", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR15624025", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR15624025/SRR15624025", "size": "2830059072", "date": "2021-08-27 15:15:27", "md5": "9e20bb27a94bdb6cf68379cf7b04f6fb", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "XS28_S4_L001_R2_001.fastq.gz", "size": "2471260273", "date": "2021-08-27 15:12:06", "md5": "54ec13987a648ce7bdd88ae6aa203dff", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "XS28_S4_L001_R1_001.fastq.gz", "size": "2431725462", "date": "2021-08-27 15:13:07", "md5": "6f773ae94d33cabfa5e3fa7c95ceac76", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "87925310"}}, "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": "8968381620"}}, "@attributes": {"alias": "GSM5538494_r1", "accession": "SRR15624025", "total_spots": "87925310", "total_bases": "8968381620", "size": "2830056861", "load_done": "true", "published": "2024-11-14 03:17:07", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR15624026", "SUBMITTER_ID": "GSM5538494_r2"}, "EXPERIMENT_REF": null, "RUN_ATTRIBUTES": {"RUN_ATTRIBUTE": {"TAG": "loader", "VALUE": "fastq-load.py", "UNITS": null}}, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS9931916", "EXTERNAL_ID": ["SAMN20994885", "GSM5538494"]}, "@attributes": {"member_name": "", "accession": "SRS9931916", "sample_name": "GSM5538494", "sample_title": "H9 hESC shLuc", "spots": "87691634", "bases": "8944546668", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR15624026.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos6/sra-pub-zq-40/SRR015/15624/SRR15624026/SRR15624026.lite.1", "size": "2337975770", "date": "2023-02-06 14:19:24", "md5": "e3000355f09aab9a2ad0c8197ba404df", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR15624026", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR15624026/SRR15624026", "size": "2842913806", "date": "2021-08-27 14:16:21", "md5": "295f09e28f81cf6d946eab939c140fef", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "XS28_S4_L002_R2_001.fastq.gz", "size": "2484903304", "date": "2021-08-27 14:15:04", "md5": "e09efd52cbb0a03ebca2f75d3092502c", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "XS28_S4_L002_R1_001.fastq.gz", "size": "2435306425", "date": "2021-08-27 14:15:36", "md5": "b351f1754ebc27c358ca420cb6746c4e", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "87691634"}}, "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": "8944546668"}}, "@attributes": {"alias": "GSM5538494_r2", "accession": "SRR15624026", "total_spots": "87691634", "total_bases": "8944546668", "size": "2842911592", "load_done": "true", "published": "2024-11-14 03:17:07", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR15624027", "SUBMITTER_ID": "GSM5538494_r3"}, "EXPERIMENT_REF": null, "RUN_ATTRIBUTES": {"RUN_ATTRIBUTE": {"TAG": "loader", "VALUE": "fastq-load.py", "UNITS": null}}, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS9931916", "EXTERNAL_ID": ["SAMN20994885", "GSM5538494"]}, "@attributes": {"member_name": "", "accession": "SRS9931916", "sample_name": "GSM5538494", "sample_title": "H9 hESC shLuc", "spots": "89775739", "bases": "9157125378", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR15624027.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos6/sra-pub-zq-40/SRR015/15624/SRR15624027/SRR15624027.lite.1", "size": "2376502329", "date": "2023-02-06 14:20:48", "md5": "daee4aeb8e362a9d36b00586f8fe8a52", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR15624027", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR15624027/SRR15624027", "size": "3231677065", "date": "2021-08-27 14:34:14", "md5": "b975528319be7bb7561339b4e81e93c6", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "XS28_S4_L003_R2_001.fastq.gz", "size": "2725959280", "date": "2021-08-27 14:29:04", "md5": "a4e9d500ac75d1058bea0b39481107ce", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "XS28_S4_L003_R1_001.fastq.gz", "size": "2745460216", "date": "2021-08-27 14:31:42", "md5": "0c0810c6b8913054d06e7dc012481827", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "89775739"}}, "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": "9157125378"}}, "@attributes": {"alias": "GSM5538494_r3", "accession": "SRR15624027", "total_spots": "89775739", "total_bases": "9157125378", "size": "3231674849", "load_done": "true", "published": "2024-11-14 03:17:07", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}]