EXPERIMENT_TITLE: GSM4038124: HiC_SNU16; 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_SNU16
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "Gastric cancer cell line"}, {"TAG": "cell line", "VALUE": "Gastric cancer cell line SNU16"}]
Pool_Member_@attributes_sample_title: HiC_SNU16
RUN_SET_RUN: [{"IDENTIFIERS": {"PRIMARY_ID": "SRR9993971", "SUBMITTER_ID": "GSM4038124_r1"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS5284971", "EXTERNAL_ID": ["SAMN12597595", "GSM4038124"]}, "@attributes": {"member_name": "", "accession": "SRS5284971", "sample_name": "GSM4038124", "sample_title": "HiC_SNU16", "spots": "350756299", "bases": "105928402298", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR9993971.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-16/SRR009/9993/SRR9993971/SRR9993971.lite.1", "size": "26507572293", "date": "2022-06-23 11:49:35", "md5": "cc89b995e497687c3b2fa480bcd3409b", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR9993971", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR9993971/SRR9993971", "size": "44271343541", "date": "2019-08-19 11:34:09", "md5": "d2fdb00efd53acc2968fda5bc8e998a9", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "HiC_SNU16_1_S1_L001_R2_001.fastq", "size": "125760456539", "date": "2019-08-19 11:13:27", "md5": "8ac78852e69485d26bd833930f0df5d2", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "HiC_SNU16_1_S1_L001_R1_001.fastq", "size": "125760456539", "date": "2019-08-19 10:44:13", "md5": "6828cba60ccaad3f4837ab1d69717ba6", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "350756299"}}, "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": "105928402298"}}, "@attributes": {"alias": "GSM4038124_r1", "accession": "SRR9993971", "total_spots": "350756299", "total_bases": "105928402298", "size": "44271342015", "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": "SRR9993972", "SUBMITTER_ID": "GSM4038124_r2"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS5284971", "EXTERNAL_ID": ["SAMN12597595", "GSM4038124"]}, "@attributes": {"member_name": "", "accession": "SRS5284971", "sample_name": "GSM4038124", "sample_title": "HiC_SNU16", "spots": "336476048", "bases": "101615766496", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "HiC_SNU16_1_S1_L002_R1_001.fastq", "size": "120638877196", "date": "2019-08-19 10:51:47", "md5": "3ff991d1ca0d206f736650280ee9a649", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "HiC_SNU16_1_S1_L002_R2_001.fastq", "size": "120638877196", "date": "2019-08-19 11:49:36", "md5": "af390dbb8083d2ab992d32fa688b88c3", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR9993972.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR009/993/SRR9993972/SRR9993972.lite.1", "size": "25426463324", "date": "2022-06-10 19:49:15", "md5": "8744a988860b759ac8a9d7f1eb140394", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR9993972", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR9993972/SRR9993972", "size": "42626352940", "date": "2019-08-19 12:45:55", "md5": "13c5c079a7c9cc693d8fc564604d133f", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "336476048"}}, "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": "101615766496"}}, "@attributes": {"alias": "GSM4038124_r2", "accession": "SRR9993972", "total_spots": "336476048", "total_bases": "101615766496", "size": "42626351410", "load_done": "true", "published": "2020-05-23 16:30:32", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}]