EXPERIMENT_TITLE: GSM3096959: A673: WT1; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Cells were fixed with formaldehyde and then the genome was digested with restriction enzyme. Proximity ligation was carried out, followed by sonication and immunoprecipitation with an antibody directed towards SMC1. Library was prepared by Tn5 transposition per nextera instructions
STUDY_DESCRIPTOR_STUDY_ABSTRACT: SMC1a HiChIP was performed for the Ewing sarcoma cell line A673 under two conditions: 1) cells treated with non-targeting CRISPR Cas9 guides or 2) STAG2-targeting CRISPR Cas9 guides. Cells treated for gene editing were clonally selected and confirmed to either express STAG2 (control condition) or have loss of STAG2 expression (STAG2 loss condition). For the control condition, we used the cell clones A673.sgNT-1c4 and the STAG2 knockout clone A673.sgSTAG2-1c6. HiChIP was performed for each clone in duplicate. Overall design: A 2x2 comparison of differential looping for SMC1 HiChIP in A673 cells +/- STAG2, mutated with Cas9
SAMPLE_TITLE: A673: WT1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "A673 cells"}, {"TAG": "cell line", "VALUE": "A673"}, {"TAG": "cell type", "VALUE": "Ewing Sarcoma"}, {"TAG": "genotype", "VALUE": "WT"}]
Pool_Member_@attributes_sample_title: A673: WT1
RUN_SET_RUN: [{"IDENTIFIERS": {"PRIMARY_ID": "SRR6997762", "SUBMITTER_ID": "GSM3096959_r1"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS3165376", "EXTERNAL_ID": ["SAMN08925019", "GSM3096959"]}, "@attributes": {"member_name": "", "accession": "SRS3165376", "sample_name": "GSM3096959", "sample_title": "A673: WT1", "spots": "129393112", "bases": "39076719824", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR6997762.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-22/SRR006/997/SRR6997762.sralite.1", "size": "9781473518", "date": "2021-06-15 04:32:59", "md5": "e232ef74e3cef3094b1bae5ff38a33cf", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR6997762", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR6997762/SRR6997762", "size": "16557975590", "date": "2018-04-13 09:42:31", "md5": "10f1f3a3646f825e35af6fdd95489f08", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}]}, "CloudFiles": {"CloudFile": [null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "129393112"}}, "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": "39076719824"}}, "@attributes": {"alias": "GSM3096959_r1", "accession": "SRR6997762", "total_spots": "129393112", "total_bases": "39076719824", "size": "16557974362", "load_done": "true", "published": "2021-05-16 09:09:08", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR6997763", "SUBMITTER_ID": "GSM3096959_r2"}, "EXPERIMENT_REF": null, "RUN_ATTRIBUTES": {"RUN_ATTRIBUTE": {"TAG": "loader", "VALUE": "fastq-load.py", "UNITS": null}}, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS3165376", "EXTERNAL_ID": ["SAMN08925019", "GSM3096959"]}, "@attributes": {"member_name": "", "accession": "SRS3165376", "sample_name": "GSM3096959", "sample_title": "A673: WT1", "spots": "22764682", "bases": "4552936400", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR6997763.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-zq-1/SRR006/6997/SRR6997763/SRR6997763.lite.1", "size": "1552183183", "date": "2022-06-14 14:53:17", "md5": "c0af792367c52145863555a73ed37061", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR6997763", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR6997763/SRR6997763", "size": "2789018506", "date": "2018-04-16 16:31:48", "md5": "0000952f5792a05f5f5b1d721a2ee76b", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}]}, "CloudFiles": {"CloudFile": [null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "22764682"}}, "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": "4552936400"}}, "@attributes": {"alias": "GSM3096959_r2", "accession": "SRR6997763", "total_spots": "22764682", "total_bases": "4552936400", "size": "2789016872", "load_done": "true", "published": "2021-05-16 09:09:07", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}]