EXPERIMENT_TITLE: GSM6167078: YL-WT-NB-ON-R14-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)
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-WT-NB-ON-R14-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-WT-NB-ON-R14-T1
RUN_SET_RUN_Pool_Member_@attributes_sample_title: YL-WT-NB-ON-R14-T1
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "YL-WT-NB-ON-R14-T1_S2_L001_R1_001.fastq.gz", "size": "792167720", "date": "2022-05-18 18:15:20", "md5": "2402efad75a4cf4dc115e15a12555128", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "YL-WT-NB-ON-R14-T1_S2_L001_R2_001.fastq.gz", "size": "862676733", "date": "2022-05-18 18:15:29", "md5": "3b6b515bd58632f59b47ad7b42b6fa59", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR19277112", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR19277112/SRR19277112", "size": "959480172", "date": "2022-05-18 18:15:50", "md5": "7a30215b8c5be10149b3c593e56a6b70", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR19277112.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-24/SRR019/19277/SRR19277112/SRR19277112.lite.1", "size": "577634760", "date": "2022-08-18 01:49:48", "md5": "e7e3222cd5214aa95a4efe5f7670796b", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]