EXPERIMENT_TITLE: GSM3262964: day15.HiC.Rep1; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Briefly, 2 million cells were cross-linked with 1% formaldehyde for 10min at RT and reaction was quenched using 125 mM of Glycine for 5 min at RT. Nuclei were isolated and directly applied for digestion using 4 cutter restriction enzyme MboI (NEB) at 37 °C o/n. All libraries were constructed using standard illumina TruSeq LT library prep.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: The three-dimensional chromatin architecture plays a critical role in the establishment of cell-type-specific gene regulatory networks in eukaryotic cells.  How pluripotent stem cells (PSC) alter their chromatin architecture to direct cell fate specification remains to be elucidated.  Here, using a human PSC cardiomyocyte differentiation model, we analyze the dynamic reorganization of chromatin structure and gene regulatory networks during key transitional stages of cardiomyocyte development.  We show that many human PSC-specific topologically associating domains (TADs) are driven by active transcription of the primate-specific retroviruses HERVH.  These HERVH are silenced at the earliest stages of differentiation , accompanied by loss of TAD borders and subsequent merging of cognate TADs during differentiation, which leads to repression of gene expression within these domains .  In line with these findings, deletion of select HERVHs results in elimination of corresponding TAD boundaries in human PSCs. We further discovered developmental stage-specific chromatin loop interactions that predict target genes of cardiac-related trait/disease non-coding genetic variants.  Overall, our results not only highlight a novel role for endogenous retroviruses in shaping species-specific PSC chromatin architecture during evolution but also provide a genomic blueprint for understanding the impact of non-coding variants in congenital and adult heart disease/traits. Overall design: hESCs are differentiated into cardiomyocyte. We used a transgenic H9 hESC line expressing a H2B-GFP fusion protein under control of the ventricular cardiomyocyte specific MYL2 promoter. We collected samples at six critical time points during differentiation: human embryonic stem cells (hESC) (Day 0), hESC mesodermal cells (Day 2), hESC-cardiac mesodermal cells (Day 5), hESC-cardiac progenitor cell (Day 7), hESC-primitive cardiomyocytes (Day 15) and hESC-ventricular cardiomyocytes (Day 80). We performed HiC, ATAC-seq, RNA-seq, and ChIP-seq for H3K27ac, H3K27me3, H3K4me1, H3K4me3, H3K9me3 and CTCF for every time point, each with two biological replicates. We also made CRISPR edited deletion at two HERV-H loci and performed RNA-seq and Hi-C, each with two replicates.
SAMPLE_TITLE: day15.HiC.Rep1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "ES derived primitive cardiomyocite"}, {"TAG": "tissue", "VALUE": "ES derived primitive cardiomyocite"}, {"TAG": "differentiation time", "VALUE": "day15"}, {"TAG": "genotype", "VALUE": "H9 MLC2v:H2B"}]
Pool_Member_@attributes_sample_title: day15.HiC.Rep1
RUN_SET_RUN: [{"IDENTIFIERS": {"PRIMARY_ID": "SRR7506541", "SUBMITTER_ID": "GSM3262964_r1"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS3533186", "EXTERNAL_ID": ["SAMN09637501", "GSM3262964"]}, "@attributes": {"member_name": "", "accession": "SRS3533186", "sample_name": "GSM3262964", "sample_title": "day15.HiC.Rep1", "spots": "206564599", "bases": "35657261503", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "run.K00168.1.SRR7506541.fastq2", "size": "53221047308", "date": "2020-02-20 18:14:05", "md5": "393ef9b1ebc1ff3ebeb34bca716b56ae", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR7506541.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-22/SRR007/506/SRR7506541.sralite.1", "size": "9279606822", "date": "2020-06-22 19:20:29", "md5": "c7f63afde08693fda391caaca1ca35a5", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR7506541", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR7506541/SRR7506541", "size": "16053035234", "date": "2018-07-30 16:16:31", "md5": "b32fb570f3411cd4d01872f39357c2f2", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "run.K00168.1.SRR7506541.fastq", "size": "38141763715", "date": "2020-02-21 03:58:33", "md5": "c4275538737b248c8da51cd936f18f0e", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "206564599"}}, "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": "35657261503"}}, "@attributes": {"alias": "GSM3262964_r1", "accession": "SRR7506541", "total_spots": "206564599", "total_bases": "35657261503", "size": "16053032816", "load_done": "true", "published": "2019-07-09 16:09:28", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR7620834", "SUBMITTER_ID": "GSM3262964_r2"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS3533186", "EXTERNAL_ID": ["SAMN09637501", "GSM3262964"]}, "@attributes": {"member_name": "", "accession": "SRS3533186", "sample_name": "GSM3262964", "sample_title": "day15.HiC.Rep1", "spots": "190799703", "bases": "32564060600", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "run.K00168.2.SRR7506541.fastq2", "size": "49158902818", "date": "2020-02-20 13:33:33", "md5": "12d878635e83e09eb8454b2a0eaa3c65", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR7620834.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-22/SRR007/620/SRR7620834.sralite.1", "size": "8466239614", "date": "2020-06-20 07:45:55", "md5": "a44ed9549dc48efc790a0c6fa09f7917", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR7620834", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR7620834/SRR7620834", "size": "14871360118", "date": "2018-07-30 15:11:52", "md5": "efe7fe1ef05d01ec21e53fe42af1a998", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "run.K00168.2.SRR7506541.fastq", "size": "34277166986", "date": "2020-02-21 06:00:20", "md5": "4e101e64ae5ece6868428af3f9b25ed6", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "190799703"}}, "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": "32564060600"}}, "@attributes": {"alias": "GSM3262964_r2", "accession": "SRR7620834", "total_spots": "190799703", "total_bases": "32564060600", "size": "14871357697", "load_done": "true", "published": "2019-07-09 16:09:29", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR7620835", "SUBMITTER_ID": "GSM3262964_r3"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS3533186", "EXTERNAL_ID": ["SAMN09637501", "GSM3262964"]}, "@attributes": {"member_name": "", "accession": "SRS3533186", "sample_name": "GSM3262964", "sample_title": "day15.HiC.Rep1", "spots": "193742534", "bases": "32803708207", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "run.K00168.3.SRR7506541.fastq", "size": "34136527930", "date": "2020-02-21 06:00:20", "md5": "32dbd914e8ef8a935fa8c03233fa5f11", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "run.K00168.3.SRR7506541.fastq2", "size": "49914980648", "date": "2020-02-20 18:14:05", "md5": "c8a93bd3de9d438f7d330e6ca236e54f", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR7620835.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-16/SRR007/620/SRR7620835.sralite.1", "size": "8532380543", "date": "2020-06-14 16:15:52", "md5": "2d15eaf7442fc26ae4eeedfea8bf25a2", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR7620835", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR7620835/SRR7620835", "size": "15211440367", "date": "2018-07-30 15:45:27", "md5": "48ac7e324577ae2bbaa0ac419d376f89", "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": "193742534"}}, "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": "32803708207"}}, "@attributes": {"alias": "GSM3262964_r3", "accession": "SRR7620835", "total_spots": "193742534", "total_bases": "32803708207", "size": "15211437949", "load_done": "true", "published": "2019-07-09 16:09:29", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR7620836", "SUBMITTER_ID": "GSM3262964_r4"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS3533186", "EXTERNAL_ID": ["SAMN09637501", "GSM3262964"]}, "@attributes": {"member_name": "", "accession": "SRS3533186", "sample_name": "GSM3262964", "sample_title": "day15.HiC.Rep1", "spots": "207399582", "bases": "35871171286", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR7620836.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-16/SRR007/620/SRR7620836.sralite.1", "size": "9332086379", "date": "2020-06-21 04:42:31", "md5": "bcd81e08e218ddf57e625876bcadeb1f", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR7620836", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR7620836/SRR7620836", "size": "16351869359", "date": "2018-07-30 15:39:58", "md5": "78a55a3d7d3cf88abe32953323049bb9", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "run.K00168.4.SRR7506541.fastq2", "size": "53434236058", "date": "2020-02-20 19:50:43", "md5": "752ab5c6d1df7af6abc38a69ffaaeeb7", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "run.K00168.4.SRR7506541.fastq", "size": "38476667012", "date": "2020-02-21 04:44:29", "md5": "20e9fca952947d32973605e75c592889", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "207399582"}}, "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": "35871171286"}}, "@attributes": {"alias": "GSM3262964_r4", "accession": "SRR7620836", "total_spots": "207399582", "total_bases": "35871171286", "size": "16351866945", "load_done": "true", "published": "2019-07-09 16:09:29", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR7620837", "SUBMITTER_ID": "GSM3262964_r5"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS3533186", "EXTERNAL_ID": ["SAMN09637501", "GSM3262964"]}, "@attributes": {"member_name": "", "accession": "SRS3533186", "sample_name": "GSM3262964", "sample_title": "day15.HiC.Rep1", "spots": "211466828", "bases": "33859652893", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "run.K00168.5.SRR7506541.fastq", "size": "32272122742", "date": "2020-02-21 04:43:49", "md5": "ee5a3c03947c155726d2522e531528a1", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR7620837.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR007/620/SRR7620837.sralite.1", "size": "8806407275", "date": "2020-06-23 16:07:27", "md5": "0a3382e5a5235e2faacadb9d913bd2a8", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR7620837", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR7620837/SRR7620837", "size": "15596994003", "date": "2018-07-30 15:17:09", "md5": "20569e20fdbb6a9858da7b51ea0609fb", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "run.K00168.5.SRR7506541.fastq2", "size": "54483025410", "date": "2020-02-20 11:08:39", "md5": "82635c2f462d04de6c5c012119f2a2b6", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "211466828"}}, "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": "33859652893"}}, "@attributes": {"alias": "GSM3262964_r5", "accession": "SRR7620837", "total_spots": "211466828", "total_bases": "33859652893", "size": "15596991581", "load_done": "true", "published": "2019-07-09 16:09:29", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR7620838", "SUBMITTER_ID": "GSM3262964_r6"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS3533186", "EXTERNAL_ID": ["SAMN09637501", "GSM3262964"]}, "@attributes": {"member_name": "", "accession": "SRS3533186", "sample_name": "GSM3262964", "sample_title": "day15.HiC.Rep1", "spots": "212794220", "bases": "33490017435", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "run.K00168.6.SRR7506541.fastq2", "size": "54826476769", "date": "2020-02-20 18:14:06", "md5": "87e791181f6af223f9bb8f883e5b8e8f", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR7620838.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR007/620/SRR7620838.sralite.1", "size": "8708847985", "date": "2020-06-22 19:12:00", "md5": "49b7fd1198fc2db0d7663ba14b74340b", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR7620838", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR7620838/SRR7620838", "size": "15462577293", "date": "2018-07-30 15:31:51", "md5": "54df8c6c26c25b843d0c88cebba139ed", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "run.K00168.6.SRR7506541.fastq", "size": "30981137400", "date": "2020-02-21 03:57:37", "md5": "5e9f7b1ad562353ab2bb09ef092847c2", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "212794220"}}, "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": "33490017435"}}, "@attributes": {"alias": "GSM3262964_r6", "accession": "SRR7620838", "total_spots": "212794220", "total_bases": "33490017435", "size": "15462574880", "load_done": "true", "published": "2019-07-09 16:09:29", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR7620839", "SUBMITTER_ID": "GSM3262964_r7"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS3533186", "EXTERNAL_ID": ["SAMN09637501", "GSM3262964"]}, "@attributes": {"member_name": "", "accession": "SRS3533186", "sample_name": "GSM3262964", "sample_title": "day15.HiC.Rep1", "spots": "99990946", "bases": "17122453645", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "run.K00168.7.SRR7506541.fastq", "size": "25748813828", "date": "2020-02-21 06:00:19", "md5": "469dc564575462897081d2cd697d812a", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR7620839.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR007/620/SRR7620839.sralite.1", "size": "4471856887", "date": "2020-06-23 15:03:38", "md5": "41d62c3822bb949ecebbe2abc2e7538c", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR7620839", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR7620839/SRR7620839", "size": "7620109031", "date": "2018-07-30 14:46:31", "md5": "bd2ef8d053013c697348ef2f4544a98c", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "run.K00168.7.SRR7506541.fastq2", "size": "39653151579", "date": "2020-02-20 10:48:56", "md5": "64bae0a77b7a130aec5c01740801cb91", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "99990946"}}, "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": "17122453645"}}, "@attributes": {"alias": "GSM3262964_r7", "accession": "SRR7620839", "total_spots": "99990946", "total_bases": "17122453645", "size": "7620106615", "load_done": "true", "published": "2019-07-09 16:09:29", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR7620840", "SUBMITTER_ID": "GSM3262964_r8"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS3533186", "EXTERNAL_ID": ["SAMN09637501", "GSM3262964"]}, "@attributes": {"member_name": "", "accession": "SRS3533186", "sample_name": "GSM3262964", "sample_title": "day15.HiC.Rep1", "spots": "115116548", "bases": "20337486136", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR7620840.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-16/SRR007/620/SRR7620840.sralite.1", "size": "5281753003", "date": "2020-06-22 05:48:41", "md5": "bd12060a934999c3a5a1a629e580fcdc", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR7620840", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR7620840/SRR7620840", "size": "8945363719", "date": "2018-07-30 14:55:16", "md5": "3abdd26efb750d754e65acb5cd731564", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "run.K00168.8.SRR7506541.fastq2", "size": "29639203245", "date": "2020-02-20 19:37:51", "md5": "5d25ba6a3174f32a1acf8c8201dae0a2", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "run.K00168.8.SRR7506541.fastq", "size": "22475844594", "date": "2020-02-21 04:08:16", "md5": "98e210b441291f68d6c1a88e6fd77c2e", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "115116548"}}, "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": "20337486136"}}, "@attributes": {"alias": "GSM3262964_r8", "accession": "SRR7620840", "total_spots": "115116548", "total_bases": "20337486136", "size": "8945361301", "load_done": "true", "published": "2019-07-09 16:09:29", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}]