EXPERIMENT_TITLE: GSM5530365: YL-NuExp4hr-shrink1hr-R3-T1; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Nuclei were purified using hytonic buffer and after treatments, nuclei were fixed for Hi-C protocol Hi-C 2.0 (PMID28435001) After cells were fixed, cells or G1 sorted cells were used for Hi-C protocol Hi-C 2.0 (PMID28435001)
STUDY_DESCRIPTOR_STUDY_ABSTRACT: We established an in vitro system to cleave cohesin in purified nuclei and this system allows us to analyze biochemcial states of cohesin in distinct chromosome structures. Overall design: Using CRISPR, we inserted 3x TEV sites to RAD21 to estalbish HAP1-RAD21-TEV cells, from which we purified nuclei and cleaved RAD21 to examine chromosome structure changes. This in vitro system allows us to examine cohesin biochemical states in different chromosome structures.
SAMPLE_TITLE: YL-NuExp4hr-shrink1hr-R3-T1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "HAP1-RAD21-TEV cells"}, {"TAG": "protocol", "VALUE": "Hi-C 2.0"}, {"TAG": "enzyme", "VALUE": "HindIII"}, {"TAG": "cell line", "VALUE": "HAP1-RAD21-TEV cells"}]
Pool_Member_@attributes_sample_title: YL-NuExp4hr-shrink1hr-R3-T1
RUN_SET_RUN: [{"IDENTIFIERS": {"PRIMARY_ID": "SRR15535115", "SUBMITTER_ID": "GSM5530365_r1"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS9846865", "EXTERNAL_ID": ["SAMN20868977", "GSM5530365"]}, "@attributes": {"member_name": "", "accession": "SRS9846865", "sample_name": "GSM5530365", "sample_title": "YL-NuExp4hr-shrink1hr-R3-T1", "spots": "59684879", "bases": "5968487900", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR15535115.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-22/SRR015/15535/SRR15535115/SRR15535115.lite.1", "size": "1503615013", "date": "2022-09-01 01:42:47", "md5": "2cfe956b8cfce6c0d5dd0ad4e5a00b25", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR15535115", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR15535115/SRR15535115", "size": "2347449329", "date": "2021-08-20 13:00:04", "md5": "fd42a761478ca499daf3b648cc797703", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "YL-NuExp4hr-shrink1hr-R3-T1_S8_L004_R2_001.fastq.gz", "size": "2078515151", "date": "2021-08-20 12:59:22", "md5": "9bf8afc052f5e099937b5ffe4fd1f593", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "YL-NuExp4hr-shrink1hr-R3-T1_S8_L004_R1_001.fastq.gz", "size": "1950577137", "date": "2021-08-20 12:58:56", "md5": "946d85c00dd2dd7af086d0147e8df69c", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "59684879"}}, "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": "5968487900"}}, "@attributes": {"alias": "GSM5530365_r1", "accession": "SRR15535115", "total_spots": "59684879", "total_bases": "5968487900", "size": "2347447799", "load_done": "true", "published": "2022-07-27 23:28:58", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR15535116", "SUBMITTER_ID": "GSM5530365_r2"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS9846865", "EXTERNAL_ID": ["SAMN20868977", "GSM5530365"]}, "@attributes": {"member_name": "", "accession": "SRS9846865", "sample_name": "GSM5530365", "sample_title": "YL-NuExp4hr-shrink1hr-R3-T1", "spots": "62038954", "bases": "6203895400", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR15535116.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-24/SRR015/15535/SRR15535116/SRR15535116.lite.1", "size": "1554291481", "date": "2022-11-14 17:03:25", "md5": "1c21f3eb835681abbea297211c325421", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR15535116", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR15535116/SRR15535116", "size": "2389347453", "date": "2021-08-20 13:05:23", "md5": "08a1f53520b03ee2f9f38cfeae34d7a1", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "YL-NuExp4hr-shrink1hr-R3-T1_S28_L006_R2_001.fastq.gz", "size": "2091745829", "date": "2021-08-20 13:04:14", "md5": "a836f7243c7f0d47f14e1bd9000025ba", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "YL-NuExp4hr-shrink1hr-R3-T1_S28_L006_R1_001.fastq.gz", "size": "2016767454", "date": "2021-08-20 13:03:33", "md5": "e2dd07bfd69b3d497872717891db2836", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "62038954"}}, "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": "6203895400"}}, "@attributes": {"alias": "GSM5530365_r2", "accession": "SRR15535116", "total_spots": "62038954", "total_bases": "6203895400", "size": "2389345921", "load_done": "true", "published": "2022-07-27 23:28:58", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR15535117", "SUBMITTER_ID": "GSM5530365_r3"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS9846865", "EXTERNAL_ID": ["SAMN20868977", "GSM5530365"]}, "@attributes": {"member_name": "", "accession": "SRS9846865", "sample_name": "GSM5530365", "sample_title": "YL-NuExp4hr-shrink1hr-R3-T1", "spots": "62147891", "bases": "6214789100", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR15535117.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-24/SRR015/15535/SRR15535117/SRR15535117.lite.1", "size": "1555890391", "date": "2022-08-26 12:52:00", "md5": "6bc9f5c09d98cdee5a81343cedcb1d9a", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR15535117", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR15535117/SRR15535117", "size": "2388699023", "date": "2021-08-20 13:06:02", "md5": "82a7d067fed2fe34cfabc01d5a82ae62", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "YL-NuExp4hr-shrink1hr-R3-T1_S34_L007_R2_001.fastq.gz", "size": "2095355839", "date": "2021-08-20 13:04:42", "md5": "4bb36c90f4262258c180493589aa4879", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "YL-NuExp4hr-shrink1hr-R3-T1_S34_L007_R1_001.fastq.gz", "size": "2009869551", "date": "2021-08-20 13:04:00", "md5": "2a5195cef7d78dcb73cd362d4780fc4c", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "62147891"}}, "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": "6214789100"}}, "@attributes": {"alias": "GSM5530365_r3", "accession": "SRR15535117", "total_spots": "62147891", "total_bases": "6214789100", "size": "2388697494", "load_done": "true", "published": "2022-07-27 23:28:58", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR15535118", "SUBMITTER_ID": "GSM5530365_r4"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS9846865", "EXTERNAL_ID": ["SAMN20868977", "GSM5530365"]}, "@attributes": {"member_name": "", "accession": "SRS9846865", "sample_name": "GSM5530365", "sample_title": "YL-NuExp4hr-shrink1hr-R3-T1", "spots": "60942617", "bases": "6094261700", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR15535118.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-22/SRR015/15535/SRR15535118/SRR15535118.lite.1", "size": "1528956828", "date": "2022-09-16 17:32:00", "md5": "efdba679d4d660c9a4e8b1eba5e3ec05", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR15535118", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR15535118/SRR15535118", "size": "2358102140", "date": "2021-08-20 13:09:42", "md5": "dbf14c9a903c2edcb86589df0d797604", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "YL-NuExp4hr-shrink1hr-R3-T1_S40_L008_R2_001.fastq.gz", "size": "2067615629", "date": "2021-08-20 13:08:26", "md5": "4f04f118cafd8d4de558786340fcc4cc", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "YL-NuExp4hr-shrink1hr-R3-T1_S40_L008_R1_001.fastq.gz", "size": "1987744517", "date": "2021-08-20 13:07:43", "md5": "ab5b0cbeaa082409e2619b778abe3d2d", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "60942617"}}, "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": "6094261700"}}, "@attributes": {"alias": "GSM5530365_r4", "accession": "SRR15535118", "total_spots": "60942617", "total_bases": "6094261700", "size": "2358100612", "load_done": "true", "published": "2022-07-27 23:28:58", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}]