EXPERIMENT_TITLE: GSM5057449: U54-HFFc6-DSG-DdeI-DpnII-20190711-R1-T1; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Nuclei was extracted by lyse cells in lysis buffer containing NP40 and protease inhibitor. DNA library was generated by biotin fill-in followed blunt end ligation. Then removal of biotin from un-ligated ends, sonication, end repair, biotin pull-down, Illumina adaptor ligation and paired end PCR. Hi-C library generated Hi-C 2.0 protocol. Belaghzal et at.2017.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Chromosome conformation capture (3C)-based assays are used to map chromatin interactions genome-wide. Quantitative analyses of chromatin interaction maps can lead to insights into the spatial organization of chromosomes and the mechanisms by which they fold. A number of protocols such as in situ Hi-C and Micro-C are now widely used and these differ in key experimental parameters including cross-linking chemistry and chromatin fragmentation strategy. To understand how the choice of experimental protocol determines the ability to detect and quantify aspects of chromosome folding we have performed a systematic evaluation of experimental parameters of 3C-based protocols. We find that different protocols capture different 3D genome features with different efficiencies. First, the use of crosslinkers such as DSG in addition to formaldehyde improves signal-to-noise allowing detection of thousands of additional loops and strengthening compartment signal. Second, fragmenting chromatin to the level of nucleosomes using MNase allows detection of more loops. On the other hand, protocols that generate larger multi-kb fragments produce stronger compartmentalization signals. We confirmed our results in multiple cell states such as pluripotent and differentiated cells as well as cell cycle stages; Mitosis and G1. Based on these insights we developed Hi-C 3.0, a single protocol that can be used to both efficiently detect chromatin loops and to quantify compartmentalization. Finally, this study produced ultra-deeply sequenced reference interaction maps using in situ Hi-C, Micro-C and Hi-C 3.0 for commonly cell lines in the 4D Nucleome Project. Overall design: 96 Hi-C and Micro-C experiments replicates included. 424 raw files and 292 processed files are used for this paper.
SAMPLE_TITLE: U54-HFFc6-DSG-DdeI-DpnII-20190711-R1-T1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "Human Foreskin Fibroblasts"}, {"TAG": "protocol", "VALUE": "in situ Hi-C"}, {"TAG": "enzyme", "VALUE": "DdeI-DpnII"}, {"TAG": "cell line", "VALUE": "HFFc6"}]
Pool_Member_@attributes_sample_title: U54-HFFc6-DSG-DdeI-DpnII-20190711-R1-T1
RUN_SET_RUN: [{"IDENTIFIERS": {"PRIMARY_ID": "SRR13601574", "SUBMITTER_ID": "GSM5057449_r1"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS8166725", "EXTERNAL_ID": ["SAMN17727293", "GSM5057449"]}, "@attributes": {"member_name": "", "accession": "SRS8166725", "sample_name": "GSM5057449", "sample_title": "U54-HFFc6-DSG-DdeI-DpnII-20190711-R1-T1", "spots": "361132819", "bases": "36113281900", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR13601574.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-24/SRR013/13601/SRR13601574/SRR13601574.lite.1", "size": "9050648831", "date": "2022-08-01 16:14:21", "md5": "3b5525a0ce27fa4ca6a7a3f49f5eee92", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR13601574", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13601574/SRR13601574", "size": "13173240503", "date": "2021-02-02 04:25:15", "md5": "af3f52d05a458fd2a197465f6caf2d04", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "U54-HFFc6-DSG-DdeI-DpnII-20190711-R1-T1_S24_L006_R2_001.fastq.gz", "size": "11162663453", "date": "2021-02-02 04:18:45", "md5": "ed6389c7c7084d9a5a14cee1676019da", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "U54-HFFc6-DSG-DdeI-DpnII-20190711-R1-T1_S24_L006_R1_001.fastq.gz", "size": "10960152532", "date": "2021-02-02 04:14:01", "md5": "591aff08b84aa9658424e3f1acf8f295", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "361132819"}}, "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": "36113281900"}}, "@attributes": {"alias": "GSM5057449_r1", "accession": "SRR13601574", "total_spots": "361132819", "total_bases": "36113281900", "size": "13173239274", "load_done": "true", "published": "2021-03-08 16:55:21", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR13601575", "SUBMITTER_ID": "GSM5057449_r2"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS8166725", "EXTERNAL_ID": ["SAMN17727293", "GSM5057449"]}, "@attributes": {"member_name": "", "accession": "SRS8166725", "sample_name": "GSM5057449", "sample_title": "U54-HFFc6-DSG-DdeI-DpnII-20190711-R1-T1", "spots": "372805734", "bases": "37280573400", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR13601575.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-24/SRR013/13601/SRR13601575/SRR13601575.lite.1", "size": "9349303690", "date": "2022-08-07 03:01:13", "md5": "1f098aaab27ca2cf55343a3655e44a7a", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR13601575", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13601575/SRR13601575", "size": "13895176706", "date": "2021-02-02 04:54:21", "md5": "3ce03247d84629a28d4b70781202982f", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "U54-HFFc6-DSG-DdeI-DpnII-20190711-R1-T1_S24_L005_R2_001.fastq.gz", "size": "11831808338", "date": "2021-02-02 04:46:21", "md5": "88e4db802a296ca581c14e273eb3cf3e", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "U54-HFFc6-DSG-DdeI-DpnII-20190711-R1-T1_S24_L005_R1_001.fastq.gz", "size": "11458699191", "date": "2021-02-02 04:41:36", "md5": "2f9fb8913bad6acfce81100b1c11ae04", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "372805734"}}, "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": "37280573400"}}, "@attributes": {"alias": "GSM5057449_r2", "accession": "SRR13601575", "total_spots": "372805734", "total_bases": "37280573400", "size": "13895175478", "load_done": "true", "published": "2021-03-08 16:55:21", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR13601576", "SUBMITTER_ID": "GSM5057449_r3"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS8166725", "EXTERNAL_ID": ["SAMN17727293", "GSM5057449"]}, "@attributes": {"member_name": "", "accession": "SRS8166725", "sample_name": "GSM5057449", "sample_title": "U54-HFFc6-DSG-DdeI-DpnII-20190711-R1-T1", "spots": "358372728", "bases": "35837272800", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR13601576.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-24/SRR013/13601/SRR13601576/SRR13601576.lite.1", "size": "8961719959", "date": "2022-08-07 02:51:28", "md5": "46bc815284d1b317c2914f821da14765", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR13601576", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13601576/SRR13601576", "size": "12744559835", "date": "2021-02-02 04:09:45", "md5": "92a1fc663fbe0d2af6cd4bc641bda11f", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "U54-HFFc6-DSG-DdeI-DpnII-20190711-R1-T1_S23_L004_R2_001.fastq.gz", "size": "10986357824", "date": "2021-02-02 04:04:31", "md5": "141f60cd368fd1ace514b54bffcc4fac", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "U54-HFFc6-DSG-DdeI-DpnII-20190711-R1-T1_S23_L004_R1_001.fastq.gz", "size": "10564845856", "date": "2021-02-02 03:55:44", "md5": "8587be19cad992873f318c8b2a9a9806", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "358372728"}}, "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": "35837272800"}}, "@attributes": {"alias": "GSM5057449_r3", "accession": "SRR13601576", "total_spots": "358372728", "total_bases": "35837272800", "size": "12744558606", "load_done": "true", "published": "2021-03-08 16:55:21", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR13601577", "SUBMITTER_ID": "GSM5057449_r4"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS8166725", "EXTERNAL_ID": ["SAMN17727293", "GSM5057449"]}, "@attributes": {"member_name": "", "accession": "SRS8166725", "sample_name": "GSM5057449", "sample_title": "U54-HFFc6-DSG-DdeI-DpnII-20190711-R1-T1", "spots": "360248813", "bases": "36024881300", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR13601577.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-24/SRR013/13601/SRR13601577/SRR13601577.lite.1", "size": "9029060267", "date": "2022-08-07 03:01:25", "md5": "d308ea7d6dd828e2888d0784df59c99a", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR13601577", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13601577/SRR13601577", "size": "13257390227", "date": "2021-02-02 04:57:54", "md5": "986fbb74295a8145a3975d87b88cc1b1", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "U54-HFFc6-DSG-DdeI-DpnII-20190711-R1-T1_S12_L008_R2_001.fastq.gz", "size": "11300775812", "date": "2021-02-02 04:45:24", "md5": "304ecbe07e24c0e2eafda6f7df51a91c", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "U54-HFFc6-DSG-DdeI-DpnII-20190711-R1-T1_S12_L008_R1_001.fastq.gz", "size": "10940339951", "date": "2021-02-02 04:32:18", "md5": "16da36e517b30e5ca6068acb77b434ba", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "360248813"}}, "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": "36024881300"}}, "@attributes": {"alias": "GSM5057449_r4", "accession": "SRR13601577", "total_spots": "360248813", "total_bases": "36024881300", "size": "13257388998", "load_done": "true", "published": "2021-03-08 16:55:21", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR13601578", "SUBMITTER_ID": "GSM5057449_r5"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS8166725", "EXTERNAL_ID": ["SAMN17727293", "GSM5057449"]}, "@attributes": {"member_name": "", "accession": "SRS8166725", "sample_name": "GSM5057449", "sample_title": "U54-HFFc6-DSG-DdeI-DpnII-20190711-R1-T1", "spots": "371052609", "bases": "37105260900", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR13601578.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-24/SRR013/13601/SRR13601578/SRR13601578.lite.1", "size": "9300603073", "date": "2022-08-07 02:54:49", "md5": "9942c32f04ce37f38bd4b2916b53fdd4", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR13601578", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13601578/SRR13601578", "size": "13641915441", "date": "2021-02-02 04:07:15", "md5": "36d7d00f67c9ae83971c31a342d6f4d3", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "U54-HFFc6-DSG-DdeI-DpnII-20190711-R1-T1_S12_L007_R2_001.fastq.gz", "size": "11647198885", "date": "2021-02-02 04:02:50", "md5": "4df9be78dc30f71185ec5ca4633ce161", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "U54-HFFc6-DSG-DdeI-DpnII-20190711-R1-T1_S12_L007_R1_001.fastq.gz", "size": "11277976805", "date": "2021-02-02 03:59:42", "md5": "f8e569c1476175d1b12fcfae8b9383d8", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "371052609"}}, "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": "37105260900"}}, "@attributes": {"alias": "GSM5057449_r5", "accession": "SRR13601578", "total_spots": "371052609", "total_bases": "37105260900", "size": "13641914209", "load_done": "true", "published": "2021-03-08 16:55:21", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR13601579", "SUBMITTER_ID": "GSM5057449_r6"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS8166725", "EXTERNAL_ID": ["SAMN17727293", "GSM5057449"]}, "@attributes": {"member_name": "", "accession": "SRS8166725", "sample_name": "GSM5057449", "sample_title": "U54-HFFc6-DSG-DdeI-DpnII-20190711-R1-T1", "spots": "375557610", "bases": "37555761000", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "U54-HFFc6-DSG-DdeI-DpnII-20190711-R1-T1_S12_L006_R1_001.fastq.gz", "size": "11306755425", "date": "2021-02-02 04:55:32", "md5": "224e72c51e2516e6b2a1d04acf44af0b", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "U54-HFFc6-DSG-DdeI-DpnII-20190711-R1-T1_S12_L006_R2_001.fastq.gz", "size": "11860425263", "date": "2021-02-02 05:02:04", "md5": "70cd986a918584dcaa07e60e1a05ac77", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR13601579", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13601579/SRR13601579", "size": "13783213223", "date": "2021-02-02 05:36:40", "md5": "dd1de4016652cee8d17d76da005ad76e", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR13601579.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-24/SRR013/13601/SRR13601579/SRR13601579.lite.1", "size": "9417814139", "date": "2022-08-01 16:40:38", "md5": "738d3bcd1bf55703de9897072420e011", "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": "375557610"}}, "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": "37555761000"}}, "@attributes": {"alias": "GSM5057449_r6", "accession": "SRR13601579", "total_spots": "375557610", "total_bases": "37555761000", "size": "13783211992", "load_done": "true", "published": "2021-03-08 16:55:21", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR13601580", "SUBMITTER_ID": "GSM5057449_r7"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS8166725", "EXTERNAL_ID": ["SAMN17727293", "GSM5057449"]}, "@attributes": {"member_name": "", "accession": "SRS8166725", "sample_name": "GSM5057449", "sample_title": "U54-HFFc6-DSG-DdeI-DpnII-20190711-R1-T1", "spots": "364494031", "bases": "36449403100", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "U54-HFFc6-DSG-DdeI-DpnII-20190711-R1-T1_S12_L005_R1_001.fastq.gz", "size": "11062923638", "date": "2021-02-02 05:21:45", "md5": "cb9ef9dbb8007cdb6c801692292f5900", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "U54-HFFc6-DSG-DdeI-DpnII-20190711-R1-T1_S12_L005_R2_001.fastq.gz", "size": "11323113147", "date": "2021-02-02 05:24:53", "md5": "44be9a56381888a34de8e9aa2b411394", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR13601580", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13601580/SRR13601580", "size": "13304059448", "date": "2021-02-02 05:33:39", "md5": "a142b672bccf78a15d2d4db0ae1b5109", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR13601580.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-24/SRR013/13601/SRR13601580/SRR13601580.lite.1", "size": "9142175900", "date": "2022-08-01 16:20:50", "md5": "90cd67de2b9012c49cc4887490165a43", "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": "364494031"}}, "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": "36449403100"}}, "@attributes": {"alias": "GSM5057449_r7", "accession": "SRR13601580", "total_spots": "364494031", "total_bases": "36449403100", "size": "13304058220", "load_done": "true", "published": "2021-03-08 16:55:21", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR13601581", "SUBMITTER_ID": "GSM5057449_r8"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS8166725", "EXTERNAL_ID": ["SAMN17727293", "GSM5057449"]}, "@attributes": {"member_name": "", "accession": "SRS8166725", "sample_name": "GSM5057449", "sample_title": "U54-HFFc6-DSG-DdeI-DpnII-20190711-R1-T1", "spots": "374383899", "bases": "37438389900", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "U54-HFFc6-DSG-DdeI-DpnII-20190711-R1-T1_S12_L004_R1_001.fastq.gz", "size": "11379082787", "date": "2021-02-02 05:47:02", "md5": "c603ea160a9fe8a5198f2156cddaf1a6", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "U54-HFFc6-DSG-DdeI-DpnII-20190711-R1-T1_S12_L004_R2_001.fastq.gz", "size": "11662348553", "date": "2021-02-02 05:51:57", "md5": "ddd6fae650a825b05cd47d318333c3ac", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR13601581", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13601581/SRR13601581", "size": "13701311810", "date": "2021-02-02 06:01:42", "md5": "41b4be0dbde2cb79c3d6cadf28f21cbc", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR13601581.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-22/SRR013/13601/SRR13601581/SRR13601581.lite.1", "size": "9388833674", "date": "2022-07-21 09:42:22", "md5": "1e3e9ac6035534d8c71d06979dec6e08", "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": "374383899"}}, "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": "37438389900"}}, "@attributes": {"alias": "GSM5057449_r8", "accession": "SRR13601581", "total_spots": "374383899", "total_bases": "37438389900", "size": "13701310580", "load_done": "true", "published": "2021-03-08 16:55:21", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR13601582", "SUBMITTER_ID": "GSM5057449_r9"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS8166725", "EXTERNAL_ID": ["SAMN17727293", "GSM5057449"]}, "@attributes": {"member_name": "", "accession": "SRS8166725", "sample_name": "GSM5057449", "sample_title": "U54-HFFc6-DSG-DdeI-DpnII-20190711-R1-T1", "spots": "370816287", "bases": "37081628700", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "U54-HFFc6-DSG-DdeI-DpnII-20190711-R1-T1_S13_L007_R1_001.fastq.gz", "size": "11425578276", "date": "2021-02-02 05:25:13", "md5": "41061ebd370dbc5fdf870278276537d9", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "U54-HFFc6-DSG-DdeI-DpnII-20190711-R1-T1_S13_L007_R2_001.fastq.gz", "size": "12390906133", "date": "2021-02-02 05:27:16", "md5": "76bd3f0b178741a7cd5293f8c098cc6b", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR13601582", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13601582/SRR13601582", "size": "14271614535", "date": "2021-02-02 05:50:09", "md5": "c044f53fa0943cf5be549e3a65f00107", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR13601582.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-24/SRR013/13601/SRR13601582/SRR13601582.lite.1", "size": "9301075343", "date": "2022-08-01 16:14:11", "md5": "56551d435af27bb564ebac0a17839708", "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": "370816287"}}, "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": "37081628700"}}, "@attributes": {"alias": "GSM5057449_r9", "accession": "SRR13601582", "total_spots": "370816287", "total_bases": "37081628700", "size": "14271613303", "load_done": "true", "published": "2021-03-08 16:55:21", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}]