EXPERIMENT_TITLE: GSM5543365: Normal cell line; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: The clinical samples were collected by needle biopsy in a 1.5µL microtube from different sites; liver, pelvic and posterier nasal space using a needle size of 16/18G Biopsy samples were falsh frozen in liquid nitogen follwod by pulverization using pre-cooled mortar and pestle. Biop-C library was generated using the Arima-HiC kit.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Our results demonstrate the utility of our Biop-C method in investigating the 3D genome organization in solid cancers, and the importance of 3D genome organization in regulating oncogenes in nasopharyngeal cancer. Overall design: We have analysed 3 nasopharyngeal cancer biopsy samples using our novel Biop-C method as well as 2 replicates of NPC cell line HK1 using arima Hi-C kit protocol. To test the reproducibility of the method, we performed Biop-C on 2 replicates of a biopsy samples. For comparision with healthy tissue, we performed hic on near normal epithelial cell line NP-69. >>>Raw data not provided for human biopsy samples due to patient privacy concerns<<<
SAMPLE_TITLE: Normal cell line
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "NP-69 cell line"}, {"TAG": "cell type", "VALUE": "Nasopharyngeal Epithelial Cell Line"}, {"TAG": "gender", "VALUE": "male"}]
Pool_Member_@attributes_sample_title: Normal cell line
RUN_SET_RUN: [{"IDENTIFIERS": {"PRIMARY_ID": "SRR15654687", "SUBMITTER_ID": "GSM5543365_r1"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS9961801", "EXTERNAL_ID": ["SAMN21022847", "GSM5543365"]}, "@attributes": {"member_name": "", "accession": "SRS9961801", "sample_name": "GSM5543365", "sample_title": "Normal cell line", "spots": "458440756", "bases": "137532226800", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "NP69_R1_L4_1.fq.gz", "size": "39801509750", "date": "2021-08-28 00:15:28", "md5": "9252c5fc0c579c68c0d328459db2e144", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "NP69_R1_L4_2.fq.gz", "size": "43894552539", "date": "2021-08-28 00:30:27", "md5": "0e8caee6425ad76522240c63ab5856bc", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR15654687", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR15654687/SRR15654687", "size": "56851283539", "date": "2021-08-28 00:45:59", "md5": "6f7ada20ba33caae32318f38f8c97c04", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR15654687.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-zq-20/SRR015/15654/SRR15654687/SRR15654687.lite.1", "size": "34629608555", "date": "2022-08-01 15:00:40", "md5": "2c0d2b06dba3d325a5b6e8efee0a70c7", "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": "458440756"}}, "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": "137532226800"}}, "@attributes": {"alias": "GSM5543365_r1", "accession": "SRR15654687", "total_spots": "458440756", "total_bases": "137532226800", "size": "56851282010", "load_done": "true", "published": "2021-09-04 11:36:47", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR15654688", "SUBMITTER_ID": "GSM5543365_r2"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS9961801", "EXTERNAL_ID": ["SAMN21022847", "GSM5543365"]}, "@attributes": {"member_name": "", "accession": "SRS9961801", "sample_name": "GSM5543365", "sample_title": "Normal cell line", "spots": "465383699", "bases": "139615109700", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR15654688.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-zq-20/SRR015/15654/SRR15654688/SRR15654688.lite.1", "size": "35215839846", "date": "2022-08-12 11:03:00", "md5": "d72d1b6500d4d319c6e28276f7b9f9f2", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR15654688", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR15654688/SRR15654688", "size": "57555481690", "date": "2021-08-30 01:30:13", "md5": "662448116bbff794d28a3747c2944918", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "NP69_R2_L5_2.fq.gz", "size": "44501558708", "date": "2021-08-30 00:48:39", "md5": "7f633f9b357adcf68b3928ff61df46ab", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "NP69_R2_L5_1.fq.gz", "size": "40390484083", "date": "2021-08-30 00:29:42", "md5": "08034ea8200585276455e3b217f748c5", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "465383699"}}, "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": "139615109700"}}, "@attributes": {"alias": "GSM5543365_r2", "accession": "SRR15654688", "total_spots": "465383699", "total_bases": "139615109700", "size": "57555480161", "load_done": "true", "published": "2021-09-04 11:36:47", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}]