EXPERIMENT_TITLE: GSM4038127: HiC_SNU1750; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Hi-C experiment were conducted in biological replicates using NlaIII, according to the protocol published by Suhas S.P. Rao et al. Cell 2014 (PMID: 25497547).  DNA libraries were prepared during Hi-C protocol according to experimental procedures described in Suhas S.P. Rao et al. Cell 2014 (PMID: 25497547).
STUDY_DESCRIPTOR_STUDY_ABSTRACT: We analysed chromatin structure alterations by EBV infection to elucidate their contribution to tumorigenesis. We performed Hi-C using gastric epithelial cells with or without EBV infection. Overall design: Hi-C experiments in 14 Gastric cancer cell lines, 2 normal gastric epithelial cells, a primary EBV(+) gastric cancer tissue, and EBV infected or uninfected gastric cancer cells.
SAMPLE_TITLE: HiC_SNU1750
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "Gastric cancer cell line"}, {"TAG": "cell line", "VALUE": "Gastric cancer cell line SNU1750"}]
Pool_Member_@attributes_sample_title: HiC_SNU1750
RUN_SET_RUN: [{"IDENTIFIERS": {"PRIMARY_ID": "SRR9993979", "SUBMITTER_ID": "GSM4038127_r1"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS5284974", "EXTERNAL_ID": ["SAMN12597592", "GSM4038127"]}, "@attributes": {"member_name": "", "accession": "SRS5284974", "sample_name": "GSM4038127", "sample_title": "HiC_SNU1750", "spots": "338860207", "bases": "102335782514", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR9993979.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-24/SRR009/9993/SRR9993979/SRR9993979.lite.1", "size": "25650587615", "date": "2022-08-05 07:37:23", "md5": "1cbcb012490fd46e85a86fdc046b69c5", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR9993979", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR9993979/SRR9993979", "size": "43048274371", "date": "2019-08-19 12:58:55", "md5": "f7f0d3a1b3d29790013a3f3c251a64df", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "HiC_SNU1750_1_S14_L003_R2_001.fastq", "size": "121494065644", "date": "2019-08-19 12:03:27", "md5": "4849abe3fa3eabe554a10a6d58a44d6e", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "HiC_SNU1750_1_S14_L003_R1_001.fastq", "size": "121494065644", "date": "2019-08-19 11:12:17", "md5": "80787104ead31e278a5221d1ce499995", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "338860207"}}, "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": "102335782514"}}, "@attributes": {"alias": "GSM4038127_r1", "accession": "SRR9993979", "total_spots": "338860207", "total_bases": "102335782514", "size": "43048272841", "load_done": "true", "published": "2020-05-23 16:30:32", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR9993980", "SUBMITTER_ID": "GSM4038127_r2"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS5284974", "EXTERNAL_ID": ["SAMN12597592", "GSM4038127"]}, "@attributes": {"member_name": "", "accession": "SRS5284974", "sample_name": "GSM4038127", "sample_title": "HiC_SNU1750", "spots": "342829346", "bases": "103534462492", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "HiC_SNU1750_2_S15_L004_R1_001.fastq", "size": "122917225156", "date": "2019-08-19 12:43:35", "md5": "ad2ab52ee2cfcc7b754addd522c1c88b", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "HiC_SNU1750_2_S15_L004_R2_001.fastq", "size": "122917225156", "date": "2019-08-19 13:50:13", "md5": "3a2d828e63ae2c6b5f194f733607e15f", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR9993980", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR9993980/SRR9993980", "size": "43564887501", "date": "2019-08-19 14:42:22", "md5": "8dcb29c8216b71f9fe7eba74dd561a6d", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR9993980.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-22/SRR009/9993/SRR9993980/SRR9993980.lite.1", "size": "25962126197", "date": "2022-07-21 15:45:11", "md5": "5550cb9aea0df20f02bb4c441f6ddced", "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": "342829346"}}, "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": "103534462492"}}, "@attributes": {"alias": "GSM4038127_r2", "accession": "SRR9993980", "total_spots": "342829346", "total_bases": "103534462492", "size": "43564885970", "load_done": "true", "published": "2020-05-23 16:30:32", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}]