EXPERIMENT_TITLE: GSM5057435: U54-ESC4DN-DSG-DpnII-20190530-R2-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-ESC4DN-DSG-DpnII-20190530-R2-T1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "Human Embryonic stem cells"}, {"TAG": "protocol", "VALUE": "in situ Hi-C"}, {"TAG": "enzyme", "VALUE": "DpnII"}, {"TAG": "cell line", "VALUE": "H1-hESC"}]
Pool_Member_@attributes_sample_title: U54-ESC4DN-DSG-DpnII-20190530-R2-T1
RUN_SET_RUN: [{"IDENTIFIERS": {"PRIMARY_ID": "SRR13601511", "SUBMITTER_ID": "GSM5057435_r1"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS8166710", "EXTERNAL_ID": ["SAMN17727307", "GSM5057435"]}, "@attributes": {"member_name": "", "accession": "SRS8166710", "sample_name": "GSM5057435", "sample_title": "U54-ESC4DN-DSG-DpnII-20190530-R2-T1", "spots": "356532010", "bases": "35653201000", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR13601511.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-24/SRR013/13601/SRR13601511/SRR13601511.lite.1", "size": "8936837600", "date": "2022-08-01 16:19:14", "md5": "a1ac8117be613ec60a5327b6a2d0774c", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR13601511", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13601511/SRR13601511", "size": "12791359632", "date": "2021-02-02 01:16:23", "md5": "ebb2889503d3d76b1612c87ca4b18027", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "U54-ESC4DN-DSG-DpnII-20190530-R2-T1_S11_L008_R2_001.fastq.gz", "size": "11043643801", "date": "2021-02-02 01:09:57", "md5": "b531b875ded110954219d1db967b2ceb", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "U54-ESC4DN-DSG-DpnII-20190530-R2-T1_S11_L008_R1_001.fastq.gz", "size": "10440662383", "date": "2021-02-02 01:04:25", "md5": "54745075b90e76a700ee67f5576387b1", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "356532010"}}, "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": "35653201000"}}, "@attributes": {"alias": "GSM5057435_r1", "accession": "SRR13601511", "total_spots": "356532010", "total_bases": "35653201000", "size": "12791358400", "load_done": "true", "published": "2021-03-08 16:55:20", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR13601512", "SUBMITTER_ID": "GSM5057435_r2"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS8166710", "EXTERNAL_ID": ["SAMN17727307", "GSM5057435"]}, "@attributes": {"member_name": "", "accession": "SRS8166710", "sample_name": "GSM5057435", "sample_title": "U54-ESC4DN-DSG-DpnII-20190530-R2-T1", "spots": "363556777", "bases": "36355677700", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR13601512.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-24/SRR013/13601/SRR13601512/SRR13601512.lite.1", "size": "9117728205", "date": "2022-08-01 16:17:48", "md5": "3c1321dd9bf202ec1ba09bef392f8996", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR13601512", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13601512/SRR13601512", "size": "13381261713", "date": "2021-02-02 00:48:45", "md5": "748f82abc87d8abf935d0095245aae61", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "U54-ESC4DN-DSG-DpnII-20190530-R2-T1_S11_L007_R2_001.fastq.gz", "size": "11324222272", "date": "2021-02-02 00:41:46", "md5": "b2b717378096589e649abaafa853796e", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "U54-ESC4DN-DSG-DpnII-20190530-R2-T1_S11_L007_R1_001.fastq.gz", "size": "11120645499", "date": "2021-02-02 00:43:38", "md5": "8b80f211fe8044b80363556c985d062a", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "363556777"}}, "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": "36355677700"}}, "@attributes": {"alias": "GSM5057435_r2", "accession": "SRR13601512", "total_spots": "363556777", "total_bases": "36355677700", "size": "13381260480", "load_done": "true", "published": "2021-03-08 16:55:20", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR13601513", "SUBMITTER_ID": "GSM5057435_r3"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS8166710", "EXTERNAL_ID": ["SAMN17727307", "GSM5057435"]}, "@attributes": {"member_name": "", "accession": "SRS8166710", "sample_name": "GSM5057435", "sample_title": "U54-ESC4DN-DSG-DpnII-20190530-R2-T1", "spots": "348045715", "bases": "34804571500", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR13601513.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-24/SRR013/13601/SRR13601513/SRR13601513.lite.1", "size": "8722103724", "date": "2022-08-07 02:57:38", "md5": "4c60a0264619e4228760d5f903779769", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR13601513", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13601513/SRR13601513", "size": "12343963844", "date": "2021-02-02 02:20:45", "md5": "e7390f7a0c5d401405994013b5fecdc8", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "U54-ESC4DN-DSG-DpnII-20190530-R2-T1_S11_L006_R2_001.fastq.gz", "size": "10539553667", "date": "2021-02-02 02:06:51", "md5": "691f84f5be4d6dda2eead4fa16589277", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "U54-ESC4DN-DSG-DpnII-20190530-R2-T1_S11_L006_R1_001.fastq.gz", "size": "10297124478", "date": "2021-02-02 01:56:20", "md5": "74aea30a67215278ef67d617428c736d", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "348045715"}}, "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": "34804571500"}}, "@attributes": {"alias": "GSM5057435_r3", "accession": "SRR13601513", "total_spots": "348045715", "total_bases": "34804571500", "size": "12343962612", "load_done": "true", "published": "2021-03-08 16:55:20", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR13601514", "SUBMITTER_ID": "GSM5057435_r4"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS8166710", "EXTERNAL_ID": ["SAMN17727307", "GSM5057435"]}, "@attributes": {"member_name": "", "accession": "SRS8166710", "sample_name": "GSM5057435", "sample_title": "U54-ESC4DN-DSG-DpnII-20190530-R2-T1", "spots": "360473406", "bases": "36047340600", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "U54-ESC4DN-DSG-DpnII-20190530-R2-T1_S11_L005_R1_001.fastq.gz", "size": "10961527637", "date": "2021-02-02 00:44:47", "md5": "da7903d2977aa53e1d63f143ddac0951", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "U54-ESC4DN-DSG-DpnII-20190530-R2-T1_S11_L005_R2_001.fastq.gz", "size": "11136086699", "date": "2021-02-02 00:49:40", "md5": "6be644d5cc16f71774c38331365d8c17", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR13601514", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13601514/SRR13601514", "size": "13143891508", "date": "2021-02-02 00:55:53", "md5": "01b22f228a0b46171c36a970c2add46d", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR13601514.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-24/SRR013/13601/SRR13601514/SRR13601514.lite.1", "size": "9041289628", "date": "2022-08-01 16:10:04", "md5": "059d551522f5d6b226b18c0b5440c61f", "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": "360473406"}}, "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": "36047340600"}}, "@attributes": {"alias": "GSM5057435_r4", "accession": "SRR13601514", "total_spots": "360473406", "total_bases": "36047340600", "size": "13143890280", "load_done": "true", "published": "2021-03-08 16:55:20", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR13601515", "SUBMITTER_ID": "GSM5057435_r5"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS8166710", "EXTERNAL_ID": ["SAMN17727307", "GSM5057435"]}, "@attributes": {"member_name": "", "accession": "SRS8166710", "sample_name": "GSM5057435", "sample_title": "U54-ESC4DN-DSG-DpnII-20190530-R2-T1", "spots": "335358898", "bases": "33535889800", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR13601515.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-22/SRR013/13601/SRR13601515/SRR13601515.lite.1", "size": "8408014397", "date": "2022-07-21 10:16:25", "md5": "784b215526fa32aafe10fe65ac844ec8", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR13601515", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13601515/SRR13601515", "size": "12971950477", "date": "2021-02-02 01:42:46", "md5": "3b5284fb911ce9a950d15db70624554b", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "U54-ESC4DN-DSG-DpnII-20190530-R2-T1_S1_L004_R2_001.fastq.gz", "size": "11056789961", "date": "2021-02-02 01:33:26", "md5": "63cdccc3ec2acf970a8c76c40a40a10b", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "U54-ESC4DN-DSG-DpnII-20190530-R2-T1_S1_L004_R1_001.fastq.gz", "size": "10552181069", "date": "2021-02-02 01:27:20", "md5": "f43e75a8b2f65a14f6194f2f7a941a6f", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "335358898"}}, "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": "33535889800"}}, "@attributes": {"alias": "GSM5057435_r5", "accession": "SRR13601515", "total_spots": "335358898", "total_bases": "33535889800", "size": "12971949250", "load_done": "true", "published": "2021-03-08 16:55:20", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR13601516", "SUBMITTER_ID": "GSM5057435_r6"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS8166710", "EXTERNAL_ID": ["SAMN17727307", "GSM5057435"]}, "@attributes": {"member_name": "", "accession": "SRS8166710", "sample_name": "GSM5057435", "sample_title": "U54-ESC4DN-DSG-DpnII-20190530-R2-T1", "spots": "364188789", "bases": "36418878900", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR13601516.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-24/SRR013/13601/SRR13601516/SRR13601516.lite.1", "size": "9129646211", "date": "2022-08-07 02:58:27", "md5": "662c77bc701bd7e4d0c4e540d5e09650", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR13601516", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13601516/SRR13601516", "size": "13780334823", "date": "2021-02-02 00:41:39", "md5": "b238438424bb2410894d654050a5a37c", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "U54-ESC4DN-DSG-DpnII-20190530-R2-T1_S1_L003_R2_001.fastq.gz", "size": "11846458054", "date": "2021-02-02 00:39:20", "md5": "a81223303ff8d55fb7a8545730bbf7af", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "U54-ESC4DN-DSG-DpnII-20190530-R2-T1_S1_L003_R1_001.fastq.gz", "size": "11127361713", "date": "2021-02-02 00:38:01", "md5": "8aa77d219f893ac8a89b3fbf45e5c297", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "364188789"}}, "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": "36418878900"}}, "@attributes": {"alias": "GSM5057435_r6", "accession": "SRR13601516", "total_spots": "364188789", "total_bases": "36418878900", "size": "13780333592", "load_done": "true", "published": "2021-03-08 16:55:20", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR13601517", "SUBMITTER_ID": "GSM5057435_r7"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS8166710", "EXTERNAL_ID": ["SAMN17727307", "GSM5057435"]}, "@attributes": {"member_name": "", "accession": "SRS8166710", "sample_name": "GSM5057435", "sample_title": "U54-ESC4DN-DSG-DpnII-20190530-R2-T1", "spots": "363810868", "bases": "36381086800", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "U54-ESC4DN-DSG-DpnII-20190530-R2-T1_S1_L002_R1_001.fastq.gz", "size": "11158343972", "date": "2021-02-02 01:27:51", "md5": "30afcaf14e8a8673aa85fb20f819cea7", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "U54-ESC4DN-DSG-DpnII-20190530-R2-T1_S1_L002_R2_001.fastq.gz", "size": "11822157164", "date": "2021-02-02 01:21:39", "md5": "10b05c41b4a7160b090a66aff7588082", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR13601517", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13601517/SRR13601517", "size": "13787871812", "date": "2021-02-02 01:39:39", "md5": "5edabef7249d37c8428724ce474a263e", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR13601517.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-24/SRR013/13601/SRR13601517/SRR13601517.lite.1", "size": "9120849536", "date": "2022-08-01 16:29:08", "md5": "38329fcf7452dc135938052ae73797fe", "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": "363810868"}}, "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": "36381086800"}}, "@attributes": {"alias": "GSM5057435_r7", "accession": "SRR13601517", "total_spots": "363810868", "total_bases": "36381086800", "size": "13787870581", "load_done": "true", "published": "2021-03-08 16:55:20", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR13601518", "SUBMITTER_ID": "GSM5057435_r8"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS8166710", "EXTERNAL_ID": ["SAMN17727307", "GSM5057435"]}, "@attributes": {"member_name": "", "accession": "SRS8166710", "sample_name": "GSM5057435", "sample_title": "U54-ESC4DN-DSG-DpnII-20190530-R2-T1", "spots": "355370082", "bases": "35537008200", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "U54-ESC4DN-DSG-DpnII-20190530-R2-T1_S1_L001_R1_001.fastq.gz", "size": "10762698005", "date": "2021-02-02 01:45:06", "md5": "f49547dde662c3b1630ceeba49af9765", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "U54-ESC4DN-DSG-DpnII-20190530-R2-T1_S1_L001_R2_001.fastq.gz", "size": "11594482492", "date": "2021-02-02 02:53:14", "md5": "f09eed7ac89f161bac1095023451c962", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR13601518", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13601518/SRR13601518", "size": "13451975591", "date": "2021-02-02 03:26:22", "md5": "187022441c64fe10db34f3e98b67e0c6", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR13601518.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-24/SRR013/13601/SRR13601518/SRR13601518.lite.1", "size": "8910071267", "date": "2022-08-01 17:02:48", "md5": "40f9e2c5291987f5810b6541dede3a85", "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": "355370082"}}, "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": "35537008200"}}, "@attributes": {"alias": "GSM5057435_r8", "accession": "SRR13601518", "total_spots": "355370082", "total_bases": "35537008200", "size": "13451974361", "load_done": "true", "published": "2021-03-08 16:55:20", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR13601519", "SUBMITTER_ID": "GSM5057435_r9"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS8166710", "EXTERNAL_ID": ["SAMN17727307", "GSM5057435"]}, "@attributes": {"member_name": "", "accession": "SRS8166710", "sample_name": "GSM5057435", "sample_title": "U54-ESC4DN-DSG-DpnII-20190530-R2-T1", "spots": "359579356", "bases": "35957935600", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR13601519.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-22/SRR013/13601/SRR13601519/SRR13601519.lite.1", "size": "9011648493", "date": "2022-07-21 09:43:39", "md5": "13fff72ba09e92e4a83ae7abecb2803d", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR13601519", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13601519/SRR13601519", "size": "13957493417", "date": "2021-02-02 02:05:57", "md5": "9af6af075ee53cd10dc8530d26149010", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "U54-ESC4DN-DSG-DpnII-20190530-R2-T1_S5_L005_R2_001.fastq.gz", "size": "11954668797", "date": "2021-02-02 01:51:37", "md5": "97515fc97e60614e590e2f38ae288d8f", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "U54-ESC4DN-DSG-DpnII-20190530-R2-T1_S5_L005_R1_001.fastq.gz", "size": "11258208674", "date": "2021-02-02 01:57:10", "md5": "c883d39bc04921cc6cc42ea2ca031111", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "359579356"}}, "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": "35957935600"}}, "@attributes": {"alias": "GSM5057435_r9", "accession": "SRR13601519", "total_spots": "359579356", "total_bases": "35957935600", "size": "13957492189", "load_done": "true", "published": "2021-03-08 16:55:20", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}]