EXPERIMENT_TITLE: GSM7790590: K562_bio4_tech1_siNC; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: RNAs were extracted 48 h after transfection. About 300,000 C2C12 cells were cross-linked and processed to generate Hi-C libraries, following modifications of established protocols. Libraries underwent paired-end sequencing on an Illumina HiSeq X Ten instrument
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Hi-C in RBFox2 knockdown K562 and RBFox2 knockout C2C12 cells, Hi-C in ActD, RNase, and RNase inhibitor (RIN) treated C2C12 cells. Overall design: Hi-C
SAMPLE_TITLE: K562_bio4_tech1_siNC
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "K562"}, {"TAG": "cell line", "VALUE": "K562"}, {"TAG": "treatment", "VALUE": "siNC"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
Pool_Member_@attributes_sample_title: K562_bio4_tech1_siNC
RUN_SET_RUN: [{"IDENTIFIERS": {"PRIMARY_ID": "SRR26109081", "EXTERNAL_ID": "GSM7790590_r1"}, "EXPERIMENT_REF": {"IDENTIFIERS": {"EXTERNAL_ID": "GSM7790590_r1"}, "@attributes": {"accession": "SRX21823269"}}, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS18923750", "EXTERNAL_ID": ["SAMN37456640", "GSM7790590"]}, "@attributes": {"member_name": "", "accession": "SRS18923750", "sample_name": "GSM7790590", "sample_title": "K562_bio4_tech1_siNC", "spots": "42477659", "bases": "12743297700", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR26109081.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos7/sra-pub-zq-41/SRR026/26109/SRR26109081/SRR26109081.lite.1", "size": "3231831293", "date": "2023-09-24 14:40:56", "md5": "8a051b44f20fc67831d6f2adfc316a8c", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR26109081", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR26109081/SRR26109081", "size": "5263558145", "date": "2023-09-19 14:17:11", "md5": "57312bdc7409ff2ccd3cc286a543a931", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "K562_bio4_tech1_siNC_combined_R2.fastq.gz", "size": "4067888598", "date": "2023-09-19 14:15:18", "md5": "c4caf713a047e565f936a566a97cde9a", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "K562_bio4_tech1_siNC_combined_R1.fastq.gz", "size": "3617952142", "date": "2023-09-19 14:14:27", "md5": "21f9ccd1d8f5aa4def53c1b796c883b1", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "42477659"}}, "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": "12743297700"}}, "@attributes": {"accession": "SRR26109081", "alias": "GSM7790590_r1", "total_spots": "42477659", "total_bases": "12743297700", "size": "5263555925", "load_done": "true", "published": "2024-12-24 00:45:20", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR26109082", "EXTERNAL_ID": "GSM7790590_r2"}, "EXPERIMENT_REF": {"IDENTIFIERS": {"EXTERNAL_ID": "GSM7790590_r1"}, "@attributes": {"accession": "SRX21823269"}}, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS18923750", "EXTERNAL_ID": ["SAMN37456640", "GSM7790590"]}, "@attributes": {"member_name": "", "accession": "SRS18923750", "sample_name": "GSM7790590", "sample_title": "K562_bio4_tech1_siNC", "spots": "84901054", "bases": "25470316200", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "K562_bio4_tech2_siNC_combined_R1.fastq.gz", "size": "8769711894", "date": "2023-09-19 14:27:24", "md5": "f77c98828b15ed8dae03f1aeebb2d069", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "K562_bio4_tech2_siNC_combined_R2.fastq.gz", "size": "8292686303", "date": "2023-09-19 14:26:51", "md5": "7749782b3cb09a64834bed8ee3481444", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR26109082", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR26109082/SRR26109082", "size": "12042204257", "date": "2023-09-19 14:29:29", "md5": "9e188dd7ef2713982afb424696c5cd1c", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR26109082.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos7/sra-pub-zq-41/SRR026/26109/SRR26109082/SRR26109082.lite.1", "size": "6426864825", "date": "2023-09-24 14:56:37", "md5": "69bbb1422dbeb7eae089a3f19144cd78", "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": "84901054"}}, "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": "25470316200"}}, "@attributes": {"accession": "SRR26109082", "alias": "GSM7790590_r2", "total_spots": "84901054", "total_bases": "25470316200", "size": "12042202036", "load_done": "true", "published": "2024-12-24 00:45:20", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}]