EXPERIMENT_TITLE: GSM5530331: YL-CTL-NB-NaCl-R6-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-CTL-NB-NaCl-R6-T1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "HAP1-RAD21-TEV cells"}, {"TAG": "protocol", "VALUE": "Hi-C 2.0"}, {"TAG": "enzyme", "VALUE": "DpnII"}, {"TAG": "cell line", "VALUE": "HAP1-RAD21-TEV cells"}]
Pool_Member_@attributes_sample_title: YL-CTL-NB-NaCl-R6-T1
RUN_SET_RUN: [{"IDENTIFIERS": {"PRIMARY_ID": "SRR15535009", "SUBMITTER_ID": "GSM5530331_r1"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS9846831", "EXTERNAL_ID": ["SAMN20869028", "GSM5530331"]}, "@attributes": {"member_name": "", "accession": "SRS9846831", "sample_name": "GSM5530331", "sample_title": "YL-CTL-NB-NaCl-R6-T1", "spots": "83123987", "bases": "8312398700", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "YL-CTL-NB-NaCl-R6-T1_S5_L003_R1_001.fastq.gz", "size": "2866879026", "date": "2021-08-20 11:54:56", "md5": "2f835a6670f244a24e1a8a3804583a64", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "YL-CTL-NB-NaCl-R6-T1_S5_L003_R2_001.fastq.gz", "size": "2999963360", "date": "2021-08-20 11:54:38", "md5": "188911ac4a142fb2c5f34d249ba6c1c9", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR15535009", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR15535009/SRR15535009", "size": "3464217741", "date": "2021-08-20 11:55:39", "md5": "b729f8071b1b5990634d8d76da97c6c7", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR15535009.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-zq-38/SRR015/15535/SRR15535009/SRR15535009.lite.1", "size": "2098462685", "date": "2022-09-30 02:34:00", "md5": "d7aa6e660a0d690ad6bf7a21db17ccee", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "83123987"}}, "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": "8312398700"}}, "@attributes": {"alias": "GSM5530331_r1", "accession": "SRR15535009", "total_spots": "83123987", "total_bases": "8312398700", "size": "3464216209", "load_done": "true", "published": "2022-07-27 23:28:57", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR15535010", "SUBMITTER_ID": "GSM5530331_r2"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS9846831", "EXTERNAL_ID": ["SAMN20869028", "GSM5530331"]}, "@attributes": {"member_name": "", "accession": "SRS9846831", "sample_name": "GSM5530331", "sample_title": "YL-CTL-NB-NaCl-R6-T1", "spots": "46818869", "bases": "4681886900", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "YL-CTL-NB-NaCl-R6-T1_S7_L004_R1_001.fastq.gz", "size": "1549495991", "date": "2021-08-20 11:48:21", "md5": "b727cd71775173b1da0b393f4f400d45", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "YL-CTL-NB-NaCl-R6-T1_S7_L004_R2_001.fastq.gz", "size": "1798800685", "date": "2021-08-20 11:48:53", "md5": "8d73398c6a9b40c036c85d3fb3775bec", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR15535010", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR15535010/SRR15535010", "size": "1968288190", "date": "2021-08-20 11:49:47", "md5": "daabb0c2485e216829cf537a5c6b5c8a", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR15535010.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-24/SRR015/15535/SRR15535010/SRR15535010.lite.1", "size": "1180853130", "date": "2022-08-26 12:50:54", "md5": "775985452bdff549fc28f566a5da62f8", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "46818869"}}, "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": "4681886900"}}, "@attributes": {"alias": "GSM5530331_r2", "accession": "SRR15535010", "total_spots": "46818869", "total_bases": "4681886900", "size": "1968286663", "load_done": "true", "published": "2022-07-27 23:28:57", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR15535011", "SUBMITTER_ID": "GSM5530331_r3"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS9846831", "EXTERNAL_ID": ["SAMN20869028", "GSM5530331"]}, "@attributes": {"member_name": "", "accession": "SRS9846831", "sample_name": "GSM5530331", "sample_title": "YL-CTL-NB-NaCl-R6-T1", "spots": "46600934", "bases": "4660093400", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "YL-CTL-NB-NaCl-R6-T1_S7_L003_R1_001.fastq.gz", "size": "1545010589", "date": "2021-08-20 11:43:06", "md5": "d7db4dd76c0d5b23d531532d6a6da619", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "YL-CTL-NB-NaCl-R6-T1_S7_L003_R2_001.fastq.gz", "size": "1787748992", "date": "2021-08-20 11:43:15", "md5": "94894f8e77b5aacd0805823de3cab677", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR15535011", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR15535011/SRR15535011", "size": "1960151252", "date": "2021-08-20 11:43:43", "md5": "b52b6726fa2d5f3523e4ed3459a8d523", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR15535011.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-24/SRR015/15535/SRR15535011/SRR15535011.lite.1", "size": "1173885220", "date": "2022-09-14 18:55:55", "md5": "c5a96c532e7488949c1b9a7f6634fc0b", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "46600934"}}, "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": "4660093400"}}, "@attributes": {"alias": "GSM5530331_r3", "accession": "SRR15535011", "total_spots": "46600934", "total_bases": "4660093400", "size": "1960149719", "load_done": "true", "published": "2022-07-27 23:28:57", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}]