{"lab": {"title": "Bing Ren, UCSD", "uuid": "795847de-20b6-4f8c-ba8d-185215469cbf", "correspondence": [{"contact_email": "YmlyZW5AdWNzZC5lZHU=", "@id": "/users/e3159ffc-a5a9-43a1-8cfa-90b776c39788/", "display_title": "Bing Ren"}], "@type": ["Lab", "Item"], "display_title": "Bing Ren, UCSD", "status": "current", "@id": "/labs/bing-ren-lab/", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.795847de-20b6-4f8c-ba8d-185215469cbf"]}}, "award": {"@id": "/awards/1UM1HG011585-01/", "uuid": "ee89349a-1d43-4048-9142-bc750f0f3b32", "status": "current", "project": "4DN", "description": "CDIMV: The transcriptional regulatory sequences communicate with each other dynamically in the 3D nuclear space to direct cell type specific gene expression. Currently, a major barrier to understanding the transcriptional regulatory programs is the lack of tools, models and maps to explore the chromatin architecture in diverse cell types and physiological contexts. We will address this pressing need by deploying transformative technologies to study the chromatin architecture in mammalian cells at an unprecedented resolution and scale. Specifically, we will generate navigable, cell-type-specific reference maps of chromatin architecture in the mouse, macaque and human brains by integrating high resolution and high throughput imaging and orthogonal single-cell-based genomic methods. We will also dissect the role of chromatin architecture in gene regulation through a set of controlled perturbation experiments in the mouse ES cells (ESC) and ESC-derived neural progenitor cells (NPC). We will develop structural models of chromatin organization with advanced polymer physics and statistical learning methods, and validate their predictive power in embryonic stem cells and in ex vivo brain slices. Finally, we will make the reference maps, analytical tools, visualization methods and structural models available to the broader community. The proposed research project will dramatically transform our ability to analyze the 4D Nucleome of complex tissues, and produce the much-needed maps, tools and models for understanding the gene regulatory programs encoded in the linear genome sequences.", "center_title": "CDIMV - Ren", "display_title": "CENTER FOR INTEGRATED MULTI-MODAL AND MULTI-SCALE NUCLEOME RESEARCH", "@type": ["Award", "Item"], "name": "1UM1HG011585-01", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "badges": [{"badge": {"display_title": "Replicate Numbers", "description": "Issues with replicate numbers", "@type": ["Badge", "Item"], "badge_classification": "Warning", "status": "released", "uuid": "24a64a84-3c33-4d76-aaf2-e5ef45eff347", "badge_icon": "/static/img/badges/replicates-orange-circle.svg", "warning": "Replicate Numbers", "title": "Replicate Numbers", "@id": "/badges/replicate-numbers/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "messages": ["Replicate set contains only a single biological replicate"]}], "status": "released", "aliases": ["bing-ren-lab:expset_scATACseq_macula_donor_3"], "accession": "4DNESTXAQTRS", "condition": "Donor 3 - macula tissue", "description": "Single cell ATAC-seq (scATACseq) in human eye, macula tissue from donor - 3", "date_created": "2024-12-02T20:41:29.694350+00:00", "submitted_by": {"error": "no view permissions"}, "dataset_label": "scATACseq (10x Multiome) in human eye tissue", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2025-06-23T19:11:58.222016+00:00"}, "public_release": "2025-06-10", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"uuid": "ec841801-cfea-4171-ab0b-a017eae93069", "@type": ["ExperimentAtacseq", "Experiment", "Item"], "status": "released", "@id": "/experiments-atacseq/4DNEXQV4ZGPY/", "display_title": "single cell ATAC-seq on macula lutea - 4DNEXQV4ZGPY", "accession": "4DNEXQV4ZGPY", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "static_headers": [{"lab": {"display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "body": "\n**Data Use Guidelines:** This is a data set generated by the \n4DN Network and made freely available to the scientific \ncommunity. If you are intending to use these data for a \npublication, we ask that you please contact the data \ngenerating lab to discuss possible coordinated publication. \nIn your manuscript, please cite the 4DN White Paper \n([doi:10.1038/nature23884](https://doi.org/10.1038/nature23884)) \nand the 4DN Data Portal paper \n([doi:10.1038/s41467-022-29697-4](https://doi.org/10.1038/s41467-022-29697-4)), \nand please acknowledge the 4DN lab which generated the data. Please direct any questions to the [Data Coordination and Integration Center](mailto:support@4dnucleome.org).", "name": "item-page-headers.ExperimentSet.data-usage-guidelines", "award": {"uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "@id": "/awards/1U01CA200059-01/", "status": "current", "@type": ["Award", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Data Usage Guidelines", "status": "released", "aliases": [], "options": {"filetype": "md", "title_icon": "exclamation-circle", "collapsible": false, "default_open": true}, "date_created": "2018-08-06T03:09:55.543206+00:00", "section_type": "Item Page Header", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2022-05-09T09:31:34.537494+00:00"}, "schema_version": "2", "@id": "/static-sections/621e8359-3885-40ce-965d-91894aa7b758/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "621e8359-3885-40ce-965d-91894aa7b758", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267228139"]}, "display_title": "Data Usage Guidelines", "external_references": [], "content": "\n**Data Use Guidelines:** This is a data set generated by the \n4DN Network and made freely available to the scientific \ncommunity. If you are intending to use these data for a \npublication, we ask that you please contact the data \ngenerating lab to discuss possible coordinated publication. \nIn your manuscript, please cite the 4DN White Paper \n([doi:10.1038/nature23884](https://doi.org/10.1038/nature23884)) \nand the 4DN Data Portal paper \n([doi:10.1038/s41467-022-29697-4](https://doi.org/10.1038/s41467-022-29697-4)), \nand please acknowledge the 4DN lab which generated the data. Please direct any questions to the [Data Coordination and Integration Center](mailto:support@4dnucleome.org).", "filetype": "md", "content_as_html": "<div class=\"markdown-container\"><p><strong>Data Use Guidelines:</strong> This is a data set generated by the \n4DN Network and made freely available to the scientific \ncommunity. If you are intending to use these data for a \npublication, we ask that you please contact the data \ngenerating lab to discuss possible coordinated publication. \nIn your manuscript, please cite the 4DN White Paper \n(<a href=\"https://doi.org/10.1038/nature23884\" rel=\"noopener noreferrer\" target=\"_blank\">doi:10.1038/nature23884</a>) \nand the 4DN Data Portal paper \n(<a href=\"https://doi.org/10.1038/s41467-022-29697-4\" rel=\"noopener noreferrer\" target=\"_blank\">doi:10.1038/s41467-022-29697-4</a>), \nand please acknowledge the 4DN lab which generated the data. Please direct any questions to the <a href=\"mailto:support@4dnucleome.org\">Data Coordination and Integration Center</a>.</p></div>"}], "project_release": "2025-06-10", "experiments_in_set": [{"status": "released", "accession": "4DNEXQV4ZGPY", "files": [{"href": "/files-fastq/4DNFIYPWC3PB/@@download/4DNFIYPWC3PB.fastq.gz", "status": "restricted", "@type": ["FileFastq", "File", "Item"], "file_classification": "raw file", "display_title": "4DNFIYPWC3PB.fastq.gz", "paired_end": "1", "upload_key": "9449eda3-dfd5-4102-9728-24af7a010a57/4DNFIYPWC3PB.fastq.gz", "accession": "4DNFIYPWC3PB", "md5sum": "f8b329508c5677608847a178453b984f", "file_size": 18903949186, "file_type": "reads", "file_type_detailed": "reads (fastq)", "uuid": "9449eda3-dfd5-4102-9728-24af7a010a57", "@id": "/files-fastq/4DNFIYPWC3PB/", "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFI13IV43V.fastq.gz", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "accession": "4DNFI13IV43V", "paired_end": "2", "uuid": "8070d9b3-4fd8-4a77-94a0-9ab7cc1131c5", "file_type": "reads", "status": "restricted", "@id": "/files-fastq/4DNFI13IV43V/", "file_format": {"display_title": "fastq", "file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"relationship_type": "grouped with", "file": {"display_title": "4DNFIH5IPMFC.fastq.gz", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "index reads (fastq)", "accession": "4DNFIH5IPMFC", "uuid": "ff207683-78ae-4133-bcfe-433bbc0d7243", "file_type": "index reads", "status": "restricted", "@id": "/files-fastq/4DNFIH5IPMFC/", "file_format": {"display_title": "fastq", "file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "lab": {"status": "current", "@type": ["Lab", "Item"], "uuid": "795847de-20b6-4f8c-ba8d-185215469cbf", "@id": "/labs/bing-ren-lab/", "name": "bing-ren-lab", "display_title": "Bing Ren, UCSD", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.795847de-20b6-4f8c-ba8d-185215469cbf"]}}, "external_references": [], "quality_metric": {"overall_quality_status": "PASS", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIYPWC3PB/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/9832404d-4123-43f3-b2a6-c353993bf7db/", "status": "released", "Total Sequences": 366087675, "display_title": "QualityMetricFastqc from 2024-12-05", "Sequence length": "101", "uuid": "9832404d-4123-43f3-b2a6-c353993bf7db", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"status": "released", "@id": "/file-formats/fastq/", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Bing Ren, UCSD", "experiment_type": "single cell ATAC-seq", "experiment_bucket": "raw file", "dataset": "scATACseq (10x Multiome) in human eye tissue", "condition": "Donor 3 - 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