EXPERIMENT_TITLE: GSM6919606: DNase Hi-C on RUES2 differentiated to mesoderm with DNaseI - 4DNEXY9AKMVH; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: description: The Official 4DN Standard in situ DNase Hi-C Protocol adapted from Ramani et al. PMID: 27685100 and approved by SC 01-16-2018 download: https://data.4dnucleome.org/protocols/1f97bb2b-180f-4a6d-b4ea-4e96c90eecdc/@@download/attachment/4DN_DNase_Hi-C_protocol_20180108.pdf
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Vascular endothelial cells are a mesoderm-derived lineage with many essential  functions, including angiogenesis and coagulation. The gene-regulatory mechanisms  underpinning endothelial specialization are largely unknown, as are the roles of  chromatin organization in regulating endothelial cell transcription. To  investigate the relationships between chromatin organization and gene expression,  we induced endothelial cell differentiation from human pluripotent stem cells and  performed Hi-C and RNA-sequencing assays at specific time points. Long-range  intrachromosomal contacts increase over the course of differentiation,  accompanied by widespread heteroeuchromatic compartment transitions that are  tightly associated with transcription. Dynamic topologically associating domain  boundaries strengthen and converge on an endothelial cell state, and function to  regulate gene expression. Chromatin pairwise point interactions (DNA loops)  increase in frequency during differentiation and are linked to the expression of  genes essential to vascular biology. Chromatin dynamics guide transcription in  endothelial cell development and promote the divergence of endothelial cells from  cardiomyocytes. Overall design: lab: Chuck Murry, UW award: 1U54DK107979-01 accession: 4DNESX5HHBRP condition: mesoderm - day 2 submitted_by: Kris Alavattam dataset_label: DNase Hi-C on human iPSCs differentiated to endothelium contributing_labs: William Noble, UW experiment_type: DNase Hi-C url: https://data.4dnucleome.org/experiment-set-replicates/4DNESX5HHBRP/ number_of_experiments: 2 experiment: 4DNEXY9AKMVH; replicate_number: Biorep 1, Techrep 1 experiment: 4DNEXAIR7YJB; replicate_number: Biorep 2, Techrep 1 Series supplementary files: *************** workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/3bc27771-c927-4989-97b1-8419cce5a7d1/ genome_assembly: GRCh38 derived_from: 4DNFI823LSII.chrom.sizes, 4DNFIUM3G3AS.pairs.gz, 4DNFIXBHYYOM.pairs.gz description: This is an output file of the Hi-C processing pipeline file_type: contact list-combined file_format: pairs file name: 4DNFI2849Y4V.pairs.gz *************** workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/3bc27771-c927-4989-97b1-8419cce5a7d1/ genome_assembly: GRCh38 derived_from: 4DNFI823LSII.chrom.sizes, 4DNFIUM3G3AS.pairs.gz, 4DNFIXBHYYOM.pairs.gz description: This is an output file of the Hi-C processing pipeline file_type: contact matrix file_format: mcool file name: 4DNFITDFDM7G.mcool *************** workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/957e0544-7b71-4a34-976f-51a6849f2085/ genome_assembly: GRCh38 derived_from: 4DNFITDFDM7G.mcool description: Boundaries calls on Hi-C contact matrices file_type: boundaries file_format: bed file name: 4DNFIV6FC82G.bed.gz *************** workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/957e0544-7b71-4a34-976f-51a6849f2085/ genome_assembly: GRCh38 derived_from: 4DNFITDFDM7G.mcool description: Diamond insulation scores calls on Hi-C contact matrices file_type: insulation score-diamond file_format: bw file name: 4DNFI4ODUZA1.bw *************** workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/8c20d591-6f65-45c7-ae78-5714d7acc9c1/ genome_assembly: GRCh38 derived_from: 4DNFITDFDM7G.mcool, 4DNFI7MCA4R6.bedGraph.gz description: Compartments signals on Hi-C contact matrices file_type: compartments file_format: bw file name: 4DNFIXYRPAMB.bw
SAMPLE_TITLE: 4D Nucleome biosample 4DNBSKVQG2RJ: RUES2
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "4D Nucleome accession", "VALUE": "4DNBSKVQG2RJ"}, {"TAG": "cell line", "VALUE": "RUES2"}, {"TAG": "sex", "VALUE": "female"}, {"TAG": "modifications summary", "VALUE": "None"}, {"TAG": "treatments summary", "VALUE": "None"}, {"TAG": "sample type", "VALUE": "in vitro differentiated cells"}, {"TAG": "biosource summary", "VALUE": "RUES2 differentiated to mesoderm"}, {"TAG": "tissue source", "VALUE": "mesoderm"}, {"TAG": "dev_stage", "VALUE": "embryonic"}, {"TAG": "biosource vendor", "VALUE": "WiCell.org"}, {"TAG": "cell culture protocols", "VALUE": "description: Protocol for passaging hPSCs and differentiating them to endothelial cells; download: https://data.4dnucleome.org/protocols/5390905f-7a27-4c82-816f-5a848c1ae21d/@@download/attachment/Alavattam-Mitzelfelt_endothelial-cells_protocol_passaging-differentiation.pdf"}]
Pool_Member_@attributes_sample_title: 4D Nucleome biosample 4DNBSKVQG2RJ: RUES2
RUN_SET_RUN: [{"IDENTIFIERS": {"PRIMARY_ID": "SRR23036938", "SUBMITTER_ID": "GSM6919606_r1"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS16478348", "EXTERNAL_ID": "SAMN32545277"}, "@attributes": {"member_name": "", "accession": "SRS16478348", "sample_name": "4D Nucleome biosample 4DNBSKVQG2RJ", "sample_title": "4D Nucleome biosample 4DNBSKVQG2RJ: RUES2", "spots": "49980925", "bases": "7497138750", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR23036938.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-24/SRR023/23036/SRR23036938/SRR23036938.lite.1", "size": "1885898625", "date": "2023-01-15 13:21:06", "md5": "05e22243ea9f9a93645fbc264d2c2720", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR23036938", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR23036938/SRR23036938", "size": "2936463337", "date": "2023-01-10 12:55:59", "md5": "6ea04da191a58daf02e1bea900c6eda9", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "4DNFICSWDSLC.fastq.gz", "size": "2430720042", "date": "2023-01-10 12:54:58", "md5": "1449d7fff0e86acc9618e4570309176f", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "4DNFI2AMFEWK.fastq.gz", "size": "2519642399", "date": "2023-01-10 12:54:34", "md5": "9bfc43b21bdbf461322dd63467af13fd", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "49980925"}}, "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": "7497138750"}}, "@attributes": {"alias": "GSM6919606_r1", "accession": "SRR23036938", "total_spots": "49980925", "total_bases": "7497138750", "size": "1885897095", "load_done": "true", "published": "2023-01-19 16:59:16", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR23036939", "SUBMITTER_ID": "GSM6919606_r2"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS16478348", "EXTERNAL_ID": "SAMN32545277"}, "@attributes": {"member_name": "", "accession": "SRS16478348", "sample_name": "4D Nucleome biosample 4DNBSKVQG2RJ", "sample_title": "4D Nucleome biosample 4DNBSKVQG2RJ: RUES2", "spots": "49239133", "bases": "7385869950", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR23036939.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-24/SRR023/23036/SRR23036939/SRR23036939.lite.1", "size": "1858165397", "date": "2023-01-15 13:21:03", "md5": "8a23e021eb4123062f6c35eba0bb1d34", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR23036939", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR23036939/SRR23036939", "size": "2845006121", "date": "2023-01-10 12:52:08", "md5": "22635c883e9ad663159e76166c871039", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "4DNFI8C7H8BT.fastq.gz", "size": "2364762798", "date": "2023-01-10 12:51:03", "md5": "e6ee18aa16a627250bf78542f8108de3", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "4DNFI385SPLG.fastq.gz", "size": "2446716776", "date": "2023-01-10 12:50:39", "md5": "32b314bc14caf6b72906be78f356fc55", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "49239133"}}, "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": "7385869950"}}, "@attributes": {"alias": "GSM6919606_r2", "accession": "SRR23036939", "total_spots": "49239133", "total_bases": "7385869950", "size": "1858163866", "load_done": "true", "published": "2023-01-19 16:59:16", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR23036940", "SUBMITTER_ID": "GSM6919606_r3"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS16478348", "EXTERNAL_ID": "SAMN32545277"}, "@attributes": {"member_name": "", "accession": "SRS16478348", "sample_name": "4D Nucleome biosample 4DNBSKVQG2RJ", "sample_title": "4D Nucleome biosample 4DNBSKVQG2RJ: RUES2", "spots": "48971927", "bases": "7345789050", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR23036940.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-24/SRR023/23036/SRR23036940/SRR23036940.lite.1", "size": "1848054841", "date": "2023-01-15 13:20:45", "md5": "6298dbc5ec8fc49bd04e7591e188d8ce", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR23036940", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR23036940/SRR23036940", "size": "2864614693", "date": "2023-01-10 12:52:28", "md5": "5b7202e209c14111ca3540ce1571b721", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "4DNFIRMYY67A.fastq.gz", "size": "2378938303", "date": "2023-01-10 12:51:15", "md5": "4b5566ee15e2c62c0ca7067bacce719b", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "4DNFILFDNQO5.fastq.gz", "size": "2454974559", "date": "2023-01-10 12:50:51", "md5": "f1522db4e21b325d669400aa293a5314", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "48971927"}}, "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": "7345789050"}}, "@attributes": {"alias": "GSM6919606_r3", "accession": "SRR23036940", "total_spots": "48971927", "total_bases": "7345789050", "size": "1848053311", "load_done": "true", "published": "2023-01-19 16:59:16", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}]