{"lab": {"title": "Bing Ren, UCSD", "correspondence": [{"contact_email": "YmlyZW5AdWNzZC5lZHU=", "@id": "/users/e3159ffc-a5a9-43a1-8cfa-90b776c39788/", "display_title": "Bing Ren"}], "display_title": "Bing Ren, UCSD", "@type": ["Lab", "Item"], "@id": "/labs/bing-ren-lab/", "status": "current", "uuid": "795847de-20b6-4f8c-ba8d-185215469cbf", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.795847de-20b6-4f8c-ba8d-185215469cbf"]}}, "award": {"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.", "status": "current", "center_title": "CDIMV - Ren", "@id": "/awards/1UM1HG011585-01/", "@type": ["Award", "Item"], "display_title": "CENTER FOR INTEGRATED MULTI-MODAL AND MULTI-SCALE NUCLEOME RESEARCH", "uuid": "ee89349a-1d43-4048-9142-bc750f0f3b32", "name": "1UM1HG011585-01", "project": "4DN", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "files": [{"file_type_detailed": "reads (fastq)", "upload_key": "076a6123-5f46-4d71-bd1f-7a3fedae9948/4DNFIFN419OF.fastq.gz", "uuid": "076a6123-5f46-4d71-bd1f-7a3fedae9948", "accession": "4DNFIFN419OF", "display_title": "4DNFIFN419OF.fastq.gz", "@id": "/files-fastq/4DNFIFN419OF/", "@type": ["FileFastq", "File", "Item"], "status": "restricted", "file_size": 11697422609, "file_classification": "raw file", "href": "/files-fastq/4DNFIFN419OF/@@download/4DNFIFN419OF.fastq.gz", "file_type": "reads", "paired_end": "1", "quality_metric": {"Sequence length": "101", "@id": "/quality-metrics-fastqc/52d6bea0-b93b-4346-ad1b-b56058596964/", "uuid": "52d6bea0-b93b-4346-ad1b-b56058596964", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIFN419OF/fastqc_report.html", "display_title": "QualityMetricFastqc from 2024-12-05", "Total Sequences": 225084662, "status": "released", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"@id": "/files-fastq/4DNFISB6B6AF/", "file_type_detailed": "reads (fastq)", "accession": "4DNFISB6B6AF", "status": "restricted", "uuid": "cbaa05fc-a405-4878-a510-36670209812c", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "paired_end": "2", "display_title": "4DNFISB6B6AF.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"relationship_type": "grouped with", "file": {"@id": "/files-fastq/4DNFIAQZ5QFV/", "file_type_detailed": "index reads (fastq)", "accession": "4DNFIAQZ5QFV", "status": "restricted", "uuid": "045f5fba-f269-4ffc-bdc4-d33e174947de", "file_type": "index reads", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIAQZ5QFV.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"file_type_detailed": "index reads (fastq)", "upload_key": "045f5fba-f269-4ffc-bdc4-d33e174947de/4DNFIAQZ5QFV.fastq.gz", "uuid": "045f5fba-f269-4ffc-bdc4-d33e174947de", "accession": "4DNFIAQZ5QFV", "display_title": "4DNFIAQZ5QFV.fastq.gz", "@id": "/files-fastq/4DNFIAQZ5QFV/", "@type": ["FileFastq", "File", "Item"], "status": "restricted", "file_size": 3952058068, "file_classification": "raw file", "href": "/files-fastq/4DNFIAQZ5QFV/@@download/4DNFIAQZ5QFV.fastq.gz", "file_type": "index reads", "quality_metric": {"Sequence length": "24", "@id": "/quality-metrics-fastqc/34cfad86-5293-4508-a21b-6f54b2d05bd2/", "uuid": "34cfad86-5293-4508-a21b-6f54b2d05bd2", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIAQZ5QFV/fastqc_report.html", "display_title": "QualityMetricFastqc from 2024-12-05", "Total Sequences": 225084662, "status": "released", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "grouped with", "file": {"@id": "/files-fastq/4DNFIFN419OF/", "file_type_detailed": "reads (fastq)", "accession": "4DNFIFN419OF", "status": "restricted", "uuid": "076a6123-5f46-4d71-bd1f-7a3fedae9948", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "paired_end": "1", "display_title": "4DNFIFN419OF.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"relationship_type": "grouped with", "file": {"@id": "/files-fastq/4DNFISB6B6AF/", "file_type_detailed": "reads (fastq)", "accession": "4DNFISB6B6AF", "status": "restricted", "uuid": "cbaa05fc-a405-4878-a510-36670209812c", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "paired_end": "2", "display_title": "4DNFISB6B6AF.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"file_type_detailed": "reads (fastq)", "upload_key": "cbaa05fc-a405-4878-a510-36670209812c/4DNFISB6B6AF.fastq.gz", "uuid": "cbaa05fc-a405-4878-a510-36670209812c", "accession": "4DNFISB6B6AF", "display_title": "4DNFISB6B6AF.fastq.gz", "@id": "/files-fastq/4DNFISB6B6AF/", "@type": ["FileFastq", "File", "Item"], "status": "restricted", "file_size": 12243236154, "file_classification": "raw file", "href": "/files-fastq/4DNFISB6B6AF/@@download/4DNFISB6B6AF.fastq.gz", "file_type": "reads", "paired_end": "2", "quality_metric": {"Sequence length": "101", "@id": "/quality-metrics-fastqc/c428c86e-4876-4bf7-a92e-2529b5cd1d0a/", "uuid": "c428c86e-4876-4bf7-a92e-2529b5cd1d0a", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFISB6B6AF/fastqc_report.html", "display_title": "QualityMetricFastqc from 2024-12-05", "Total Sequences": 225084662, "status": "released", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"@id": "/files-fastq/4DNFIFN419OF/", "file_type_detailed": "reads (fastq)", "accession": "4DNFIFN419OF", "status": "restricted", "uuid": "076a6123-5f46-4d71-bd1f-7a3fedae9948", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "paired_end": "1", "display_title": "4DNFIFN419OF.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"relationship_type": "grouped with", "file": {"@id": "/files-fastq/4DNFIAQZ5QFV/", "file_type_detailed": "index reads (fastq)", "accession": "4DNFIAQZ5QFV", "status": "restricted", "uuid": "045f5fba-f269-4ffc-bdc4-d33e174947de", "file_type": "index reads", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIAQZ5QFV.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"file_type_detailed": "index reads (fastq)", "upload_key": "13b4b083-ee09-43ad-b7a0-de880197c188/4DNFIOYQFHZ6.fastq.gz", "uuid": "13b4b083-ee09-43ad-b7a0-de880197c188", "accession": "4DNFIOYQFHZ6", "display_title": "4DNFIOYQFHZ6.fastq.gz", "@id": "/files-fastq/4DNFIOYQFHZ6/", "@type": ["FileFastq", "File", "Item"], "status": "restricted", "file_size": 12569382, "file_classification": "raw file", "href": "/files-fastq/4DNFIOYQFHZ6/@@download/4DNFIOYQFHZ6.fastq.gz", "file_type": "index reads", "quality_metric": {"Sequence length": "8", "@id": "/quality-metrics-fastqc/5fd8d767-657e-4b8f-ac1f-08f847bff154/", "uuid": "5fd8d767-657e-4b8f-ac1f-08f847bff154", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIOYQFHZ6/fastqc_report.html", "display_title": "QualityMetricFastqc from 2024-12-05", "Total Sequences": 1508048, "status": "released", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "grouped with", "file": {"@id": "/files-fastq/4DNFI43QZ53D/", "file_type_detailed": "reads (fastq)", "accession": "4DNFI43QZ53D", "status": "restricted", "uuid": "b61db21a-088d-433d-a4e6-9d6a82ff23b5", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "paired_end": "1", "display_title": "4DNFI43QZ53D.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"relationship_type": "grouped with", "file": {"@id": "/files-fastq/4DNFI5L938YA/", "file_type_detailed": "reads (fastq)", "accession": "4DNFI5L938YA", "status": "restricted", "uuid": "07580691-ef84-43da-af52-3e4ad70448b2", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "paired_end": "2", "display_title": "4DNFI5L938YA.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"file_type_detailed": "reads (fastq)", "upload_key": "b61db21a-088d-433d-a4e6-9d6a82ff23b5/4DNFI43QZ53D.fastq.gz", "uuid": "b61db21a-088d-433d-a4e6-9d6a82ff23b5", "accession": "4DNFI43QZ53D", "display_title": "4DNFI43QZ53D.fastq.gz", "@id": "/files-fastq/4DNFI43QZ53D/", "@type": ["FileFastq", "File", "Item"], "status": "restricted", "file_size": 53311815, "file_classification": "raw file", "href": "/files-fastq/4DNFI43QZ53D/@@download/4DNFI43QZ53D.fastq.gz", "file_type": "reads", "paired_end": "1", "quality_metric": {"Sequence length": "50", "@id": "/quality-metrics-fastqc/9cac074b-8dfb-411d-b89d-3e38b507bd55/", "uuid": "9cac074b-8dfb-411d-b89d-3e38b507bd55", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI43QZ53D/fastqc_report.html", "display_title": "QualityMetricFastqc from 2024-12-05", "Total Sequences": 1508048, "status": "released", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"@id": "/files-fastq/4DNFI5L938YA/", "file_type_detailed": "reads (fastq)", "accession": "4DNFI5L938YA", "status": "restricted", "uuid": "07580691-ef84-43da-af52-3e4ad70448b2", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "paired_end": "2", "display_title": "4DNFI5L938YA.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"relationship_type": "grouped with", "file": {"@id": "/files-fastq/4DNFIOYQFHZ6/", "file_type_detailed": "index reads (fastq)", "accession": "4DNFIOYQFHZ6", "status": "restricted", "uuid": "13b4b083-ee09-43ad-b7a0-de880197c188", "file_type": "index reads", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIOYQFHZ6.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"relationship_type": "grouped with", "file": {"@id": "/files-fastq/4DNFI26RUNNY/", "file_type_detailed": "index reads (fastq)", "accession": "4DNFI26RUNNY", "status": "restricted", "uuid": "793958e3-4982-452c-a063-9ed003dc222f", "file_type": "index reads", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFI26RUNNY.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"file_type_detailed": "index reads (fastq)", "upload_key": "793958e3-4982-452c-a063-9ed003dc222f/4DNFI26RUNNY.fastq.gz", "uuid": "793958e3-4982-452c-a063-9ed003dc222f", "accession": "4DNFI26RUNNY", "display_title": "4DNFI26RUNNY.fastq.gz", "@id": "/files-fastq/4DNFI26RUNNY/", "@type": ["FileFastq", "File", "Item"], "status": "restricted", "file_size": 27993604, "file_classification": "raw file", "href": "/files-fastq/4DNFI26RUNNY/@@download/4DNFI26RUNNY.fastq.gz", "file_type": "index reads", "quality_metric": {"Sequence length": "16", "@id": "/quality-metrics-fastqc/5ed472b3-ff56-46b7-86d0-1d8ed34c52b9/", "uuid": "5ed472b3-ff56-46b7-86d0-1d8ed34c52b9", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI26RUNNY/fastqc_report.html", "display_title": "QualityMetricFastqc from 2024-12-05", "Total Sequences": 1508048, "status": "released", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "grouped with", "file": {"@id": "/files-fastq/4DNFI43QZ53D/", "file_type_detailed": "reads (fastq)", "accession": "4DNFI43QZ53D", "status": "restricted", "uuid": "b61db21a-088d-433d-a4e6-9d6a82ff23b5", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "paired_end": "1", "display_title": "4DNFI43QZ53D.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"relationship_type": "grouped with", "file": {"@id": "/files-fastq/4DNFI5L938YA/", "file_type_detailed": "reads (fastq)", "accession": "4DNFI5L938YA", "status": "restricted", "uuid": "07580691-ef84-43da-af52-3e4ad70448b2", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "paired_end": "2", "display_title": "4DNFI5L938YA.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"file_type_detailed": "reads (fastq)", "upload_key": "07580691-ef84-43da-af52-3e4ad70448b2/4DNFI5L938YA.fastq.gz", "uuid": "07580691-ef84-43da-af52-3e4ad70448b2", "accession": "4DNFI5L938YA", "display_title": "4DNFI5L938YA.fastq.gz", "@id": "/files-fastq/4DNFI5L938YA/", "@type": ["FileFastq", "File", "Item"], "status": "restricted", "file_size": 55053463, "file_classification": "raw file", "href": "/files-fastq/4DNFI5L938YA/@@download/4DNFI5L938YA.fastq.gz", "file_type": "reads", "paired_end": "2", "quality_metric": {"Sequence length": "50", "@id": "/quality-metrics-fastqc/fae930d9-1592-4b2a-b807-72beb137bbab/", "uuid": "fae930d9-1592-4b2a-b807-72beb137bbab", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI5L938YA/fastqc_report.html", "display_title": "QualityMetricFastqc from 2024-12-05", "Total Sequences": 1508048, "status": "released", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"@id": "/files-fastq/4DNFI43QZ53D/", "file_type_detailed": "reads (fastq)", "accession": "4DNFI43QZ53D", "status": "restricted", "uuid": "b61db21a-088d-433d-a4e6-9d6a82ff23b5", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "paired_end": "1", "display_title": "4DNFI43QZ53D.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"relationship_type": "grouped with", "file": {"@id": "/files-fastq/4DNFIOYQFHZ6/", "file_type_detailed": "index reads (fastq)", "accession": "4DNFIOYQFHZ6", "status": "restricted", "uuid": "13b4b083-ee09-43ad-b7a0-de880197c188", "file_type": "index reads", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIOYQFHZ6.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"relationship_type": "grouped with", "file": {"@id": "/files-fastq/4DNFI26RUNNY/", "file_type_detailed": "index reads (fastq)", "accession": "4DNFI26RUNNY", "status": "restricted", "uuid": "793958e3-4982-452c-a063-9ed003dc222f", "file_type": "index reads", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFI26RUNNY.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"file_type_detailed": "index reads (fastq)", "upload_key": "8ccee03f-af2d-44e9-8949-a32ea53760da/4DNFIMJX4N9M.fastq.gz", "uuid": "8ccee03f-af2d-44e9-8949-a32ea53760da", "accession": "4DNFIMJX4N9M", "display_title": "4DNFIMJX4N9M.fastq.gz", "@id": "/files-fastq/4DNFIMJX4N9M/", "@type": ["FileFastq", "File", "Item"], "status": "restricted", "file_size": 12640354, "file_classification": "raw file", "href": "/files-fastq/4DNFIMJX4N9M/@@download/4DNFIMJX4N9M.fastq.gz", "file_type": "index reads", "quality_metric": {"Sequence length": "8", "@id": "/quality-metrics-fastqc/1b96ddc2-69e3-4232-baf0-482a0d5703e7/", "uuid": "1b96ddc2-69e3-4232-baf0-482a0d5703e7", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIMJX4N9M/fastqc_report.html", "display_title": "QualityMetricFastqc from 2024-12-05", "Total Sequences": 1506614, "status": "released", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "grouped with", "file": {"@id": "/files-fastq/4DNFIE7B63JB/", "file_type_detailed": "reads (fastq)", "accession": "4DNFIE7B63JB", "status": "restricted", "uuid": "eba56a38-6b85-4037-8c51-995eab81019e", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "paired_end": "1", "display_title": "4DNFIE7B63JB.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"relationship_type": "grouped with", "file": {"@id": "/files-fastq/4DNFI17CSYLH/", "file_type_detailed": "reads (fastq)", "accession": "4DNFI17CSYLH", "status": "restricted", "uuid": "9cb3bd36-c19f-4d29-b534-7f3899bdeba1", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "paired_end": "2", "display_title": "4DNFI17CSYLH.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"file_type_detailed": "reads (fastq)", "upload_key": "eba56a38-6b85-4037-8c51-995eab81019e/4DNFIE7B63JB.fastq.gz", "uuid": "eba56a38-6b85-4037-8c51-995eab81019e", "accession": "4DNFIE7B63JB", "display_title": "4DNFIE7B63JB.fastq.gz", "@id": "/files-fastq/4DNFIE7B63JB/", "@type": ["FileFastq", "File", "Item"], "status": "restricted", "file_size": 53062922, "file_classification": "raw file", "href": "/files-fastq/4DNFIE7B63JB/@@download/4DNFIE7B63JB.fastq.gz", "file_type": "reads", "paired_end": "1", "quality_metric": {"Sequence length": "50", "@id": "/quality-metrics-fastqc/cd337316-2815-48a4-b90a-bc7a4220f1f0/", "uuid": "cd337316-2815-48a4-b90a-bc7a4220f1f0", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIE7B63JB/fastqc_report.html", "display_title": "QualityMetricFastqc from 2024-12-05", "Total Sequences": 1506614, "status": "released", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"@id": "/files-fastq/4DNFI17CSYLH/", "file_type_detailed": "reads (fastq)", "accession": "4DNFI17CSYLH", "status": "restricted", "uuid": "9cb3bd36-c19f-4d29-b534-7f3899bdeba1", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "paired_end": "2", "display_title": "4DNFI17CSYLH.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"relationship_type": "grouped with", "file": {"@id": "/files-fastq/4DNFIMJX4N9M/", "file_type_detailed": "index reads (fastq)", "accession": "4DNFIMJX4N9M", "status": "restricted", "uuid": "8ccee03f-af2d-44e9-8949-a32ea53760da", "file_type": "index reads", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIMJX4N9M.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"relationship_type": "grouped with", "file": {"@id": "/files-fastq/4DNFIYJU2NM6/", "file_type_detailed": "index reads (fastq)", "accession": "4DNFIYJU2NM6", "status": "restricted", "uuid": "79cc3108-3499-4697-8d10-8d8a22c62f97", "file_type": "index reads", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIYJU2NM6.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"file_type_detailed": "index reads (fastq)", "upload_key": "79cc3108-3499-4697-8d10-8d8a22c62f97/4DNFIYJU2NM6.fastq.gz", "uuid": "79cc3108-3499-4697-8d10-8d8a22c62f97", "accession": "4DNFIYJU2NM6", "display_title": "4DNFIYJU2NM6.fastq.gz", "@id": "/files-fastq/4DNFIYJU2NM6/", "@type": ["FileFastq", "File", "Item"], "status": "restricted", "file_size": 28410903, "file_classification": "raw file", "href": "/files-fastq/4DNFIYJU2NM6/@@download/4DNFIYJU2NM6.fastq.gz", "file_type": "index reads", "quality_metric": {"Sequence length": "16", "@id": "/quality-metrics-fastqc/3346be07-5452-4d44-804f-3861fea08393/", "uuid": "3346be07-5452-4d44-804f-3861fea08393", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIYJU2NM6/fastqc_report.html", "display_title": "QualityMetricFastqc from 2024-12-05", "Total Sequences": 1506614, "status": "released", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "grouped with", "file": {"@id": "/files-fastq/4DNFIE7B63JB/", "file_type_detailed": "reads (fastq)", "accession": "4DNFIE7B63JB", "status": "restricted", "uuid": "eba56a38-6b85-4037-8c51-995eab81019e", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "paired_end": "1", "display_title": "4DNFIE7B63JB.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"relationship_type": "grouped with", "file": {"@id": "/files-fastq/4DNFI17CSYLH/", "file_type_detailed": "reads (fastq)", "accession": "4DNFI17CSYLH", "status": "restricted", "uuid": "9cb3bd36-c19f-4d29-b534-7f3899bdeba1", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "paired_end": "2", "display_title": "4DNFI17CSYLH.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"file_type_detailed": "reads (fastq)", "upload_key": "9cb3bd36-c19f-4d29-b534-7f3899bdeba1/4DNFI17CSYLH.fastq.gz", "uuid": "9cb3bd36-c19f-4d29-b534-7f3899bdeba1", "accession": "4DNFI17CSYLH", "display_title": "4DNFI17CSYLH.fastq.gz", "@id": "/files-fastq/4DNFI17CSYLH/", "@type": ["FileFastq", "File", "Item"], "status": "restricted", "file_size": 54910703, "file_classification": "raw file", "href": "/files-fastq/4DNFI17CSYLH/@@download/4DNFI17CSYLH.fastq.gz", "file_type": "reads", "paired_end": "2", "quality_metric": {"Sequence length": "50", "@id": "/quality-metrics-fastqc/93f81ab5-fa8d-487c-a727-cb7a953ba7b2/", "uuid": "93f81ab5-fa8d-487c-a727-cb7a953ba7b2", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI17CSYLH/fastqc_report.html", "display_title": "QualityMetricFastqc from 2024-12-05", "Total Sequences": 1506614, "status": "released", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"@id": "/files-fastq/4DNFIE7B63JB/", "file_type_detailed": "reads (fastq)", "accession": "4DNFIE7B63JB", "status": "restricted", "uuid": "eba56a38-6b85-4037-8c51-995eab81019e", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "paired_end": "1", "display_title": "4DNFIE7B63JB.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"relationship_type": "grouped with", "file": {"@id": "/files-fastq/4DNFIMJX4N9M/", "file_type_detailed": "index reads (fastq)", "accession": "4DNFIMJX4N9M", "status": "restricted", "uuid": "8ccee03f-af2d-44e9-8949-a32ea53760da", "file_type": "index reads", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIMJX4N9M.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"relationship_type": "grouped with", "file": {"@id": "/files-fastq/4DNFIYJU2NM6/", "file_type_detailed": "index reads (fastq)", "accession": "4DNFIYJU2NM6", "status": "restricted", "uuid": "79cc3108-3499-4697-8d10-8d8a22c62f97", "file_type": "index reads", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIYJU2NM6.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"file_type_detailed": "index reads (fastq)", "upload_key": "039424c1-6945-4494-ad03-1730853f8f92/4DNFIYSOKY55.fastq.gz", "uuid": "039424c1-6945-4494-ad03-1730853f8f92", "accession": "4DNFIYSOKY55", "display_title": "4DNFIYSOKY55.fastq.gz", "@id": "/files-fastq/4DNFIYSOKY55/", "@type": ["FileFastq", "File", "Item"], "status": "restricted", "file_size": 13312570, "file_classification": "raw file", "href": "/files-fastq/4DNFIYSOKY55/@@download/4DNFIYSOKY55.fastq.gz", "file_type": "index reads", "quality_metric": {"Sequence length": "8", "@id": "/quality-metrics-fastqc/a6eecc6c-49d5-4561-924e-ac2371570700/", "uuid": "a6eecc6c-49d5-4561-924e-ac2371570700", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIYSOKY55/fastqc_report.html", "display_title": "QualityMetricFastqc from 2024-12-05", "Total Sequences": 1575595, "status": "released", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "grouped with", "file": {"@id": "/files-fastq/4DNFI9T7LHGI/", "file_type_detailed": "reads (fastq)", "accession": "4DNFI9T7LHGI", "status": "restricted", "uuid": "529a6141-f9f3-4cd3-baa9-09820eafc299", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "paired_end": "1", "display_title": "4DNFI9T7LHGI.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"relationship_type": "grouped with", "file": {"@id": "/files-fastq/4DNFITDGM5DO/", "file_type_detailed": "reads (fastq)", "accession": "4DNFITDGM5DO", "status": "restricted", "uuid": "cd9736b8-6405-402e-bdb6-5c86551b445a", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "paired_end": "2", "display_title": "4DNFITDGM5DO.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"file_type_detailed": "reads (fastq)", "upload_key": "529a6141-f9f3-4cd3-baa9-09820eafc299/4DNFI9T7LHGI.fastq.gz", "uuid": "529a6141-f9f3-4cd3-baa9-09820eafc299", "accession": "4DNFI9T7LHGI", "display_title": "4DNFI9T7LHGI.fastq.gz", "@id": "/files-fastq/4DNFI9T7LHGI/", "@type": ["FileFastq", "File", "Item"], "status": "restricted", "file_size": 55931181, "file_classification": "raw file", "href": "/files-fastq/4DNFI9T7LHGI/@@download/4DNFI9T7LHGI.fastq.gz", "file_type": "reads", "paired_end": "1", "quality_metric": {"Sequence length": "50", "@id": "/quality-metrics-fastqc/5a00ea57-38ae-4ff9-a50f-f66671ca2f8c/", "uuid": "5a00ea57-38ae-4ff9-a50f-f66671ca2f8c", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI9T7LHGI/fastqc_report.html", "display_title": "QualityMetricFastqc from 2024-12-05", "Total Sequences": 1575595, "status": "released", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"@id": "/files-fastq/4DNFITDGM5DO/", "file_type_detailed": "reads (fastq)", "accession": "4DNFITDGM5DO", "status": "restricted", "uuid": "cd9736b8-6405-402e-bdb6-5c86551b445a", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "paired_end": "2", "display_title": "4DNFITDGM5DO.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"relationship_type": "grouped with", "file": {"@id": "/files-fastq/4DNFIYSOKY55/", "file_type_detailed": "index reads (fastq)", "accession": "4DNFIYSOKY55", "status": "restricted", "uuid": "039424c1-6945-4494-ad03-1730853f8f92", "file_type": "index reads", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIYSOKY55.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"relationship_type": "grouped with", "file": {"@id": "/files-fastq/4DNFIE4A7Q7E/", "file_type_detailed": "index reads (fastq)", "accession": "4DNFIE4A7Q7E", "status": "restricted", "uuid": "a3f46eed-3ebf-48d6-8141-4aeead5185ea", "file_type": "index reads", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIE4A7Q7E.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"file_type_detailed": "index reads (fastq)", "upload_key": "a3f46eed-3ebf-48d6-8141-4aeead5185ea/4DNFIE4A7Q7E.fastq.gz", "uuid": "a3f46eed-3ebf-48d6-8141-4aeead5185ea", "accession": "4DNFIE4A7Q7E", "display_title": "4DNFIE4A7Q7E.fastq.gz", "@id": "/files-fastq/4DNFIE4A7Q7E/", "@type": ["FileFastq", "File", "Item"], "status": "restricted", "file_size": 29466801, "file_classification": "raw file", "href": "/files-fastq/4DNFIE4A7Q7E/@@download/4DNFIE4A7Q7E.fastq.gz", "file_type": "index reads", "quality_metric": {"Sequence length": "16", "@id": "/quality-metrics-fastqc/1a7cec32-4189-47bf-b467-4ab241eba3bd/", "uuid": "1a7cec32-4189-47bf-b467-4ab241eba3bd", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIE4A7Q7E/fastqc_report.html", "display_title": "QualityMetricFastqc from 2024-12-05", "Total Sequences": 1575595, "status": "released", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "grouped with", "file": {"@id": "/files-fastq/4DNFI9T7LHGI/", "file_type_detailed": "reads (fastq)", "accession": "4DNFI9T7LHGI", "status": "restricted", "uuid": "529a6141-f9f3-4cd3-baa9-09820eafc299", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "paired_end": "1", "display_title": "4DNFI9T7LHGI.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"relationship_type": "grouped with", "file": {"@id": "/files-fastq/4DNFITDGM5DO/", "file_type_detailed": "reads (fastq)", "accession": "4DNFITDGM5DO", "status": "restricted", "uuid": "cd9736b8-6405-402e-bdb6-5c86551b445a", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "paired_end": "2", "display_title": "4DNFITDGM5DO.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"file_type_detailed": "reads (fastq)", "upload_key": "cd9736b8-6405-402e-bdb6-5c86551b445a/4DNFITDGM5DO.fastq.gz", "uuid": "cd9736b8-6405-402e-bdb6-5c86551b445a", "accession": "4DNFITDGM5DO", "display_title": "4DNFITDGM5DO.fastq.gz", "@id": "/files-fastq/4DNFITDGM5DO/", "@type": ["FileFastq", "File", "Item"], "status": "restricted", "file_size": 57917131, "file_classification": "raw file", "href": "/files-fastq/4DNFITDGM5DO/@@download/4DNFITDGM5DO.fastq.gz", "file_type": "reads", "paired_end": "2", "quality_metric": {"Sequence length": "50", "@id": "/quality-metrics-fastqc/5be005df-9bd8-43d6-89bd-7e67300d3d6d/", "uuid": "5be005df-9bd8-43d6-89bd-7e67300d3d6d", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFITDGM5DO/fastqc_report.html", "display_title": "QualityMetricFastqc from 2024-12-05", "Total Sequences": 1575595, "status": "released", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"@id": "/files-fastq/4DNFI9T7LHGI/", "file_type_detailed": "reads (fastq)", "accession": "4DNFI9T7LHGI", "status": "restricted", "uuid": "529a6141-f9f3-4cd3-baa9-09820eafc299", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "paired_end": "1", "display_title": "4DNFI9T7LHGI.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"relationship_type": "grouped with", "file": {"@id": "/files-fastq/4DNFIYSOKY55/", "file_type_detailed": "index reads (fastq)", "accession": "4DNFIYSOKY55", "status": "restricted", "uuid": "039424c1-6945-4494-ad03-1730853f8f92", "file_type": "index reads", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIYSOKY55.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"relationship_type": "grouped with", "file": {"@id": "/files-fastq/4DNFIE4A7Q7E/", "file_type_detailed": "index reads (fastq)", "accession": "4DNFIE4A7Q7E", "status": "restricted", "uuid": "a3f46eed-3ebf-48d6-8141-4aeead5185ea", "file_type": "index reads", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIE4A7Q7E.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"file_type_detailed": "index reads (fastq)", "upload_key": "6fb253ac-05c4-44ca-bab0-ca31a214dfd1/4DNFIHRYZ9XG.fastq.gz", "uuid": "6fb253ac-05c4-44ca-bab0-ca31a214dfd1", "accession": "4DNFIHRYZ9XG", "display_title": "4DNFIHRYZ9XG.fastq.gz", "@id": "/files-fastq/4DNFIHRYZ9XG/", "@type": ["FileFastq", "File", "Item"], "status": "restricted", "file_size": 12625087, "file_classification": "raw file", "href": "/files-fastq/4DNFIHRYZ9XG/@@download/4DNFIHRYZ9XG.fastq.gz", "file_type": "index reads", "quality_metric": {"Sequence length": "8", "@id": "/quality-metrics-fastqc/feae5771-0fc2-4a16-b17a-d1a70dd873ca/", "uuid": "feae5771-0fc2-4a16-b17a-d1a70dd873ca", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIHRYZ9XG/fastqc_report.html", "display_title": "QualityMetricFastqc from 2024-12-05", "Total Sequences": 1500127, "status": "released", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "grouped with", "file": {"@id": "/files-fastq/4DNFIKJHNZTR/", "file_type_detailed": "reads (fastq)", "accession": "4DNFIKJHNZTR", "status": "restricted", "uuid": "bdd093e2-3f38-4037-82f9-b2911a0d5474", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "paired_end": "1", "display_title": "4DNFIKJHNZTR.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"relationship_type": "grouped with", "file": {"@id": "/files-fastq/4DNFIKR3QSG2/", "file_type_detailed": "reads (fastq)", "accession": "4DNFIKR3QSG2", "status": "restricted", "uuid": "75d2f7ec-25e5-41a0-9472-3ed004dd8177", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "paired_end": "2", "display_title": "4DNFIKR3QSG2.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"file_type_detailed": "reads (fastq)", "upload_key": "bdd093e2-3f38-4037-82f9-b2911a0d5474/4DNFIKJHNZTR.fastq.gz", "uuid": "bdd093e2-3f38-4037-82f9-b2911a0d5474", "accession": "4DNFIKJHNZTR", "display_title": "4DNFIKJHNZTR.fastq.gz", "@id": "/files-fastq/4DNFIKJHNZTR/", "@type": ["FileFastq", "File", "Item"], "status": "restricted", "file_size": 52576629, "file_classification": "raw file", "href": "/files-fastq/4DNFIKJHNZTR/@@download/4DNFIKJHNZTR.fastq.gz", "file_type": "reads", "paired_end": "1", "quality_metric": {"Sequence length": "50", "@id": "/quality-metrics-fastqc/13e27425-6a69-46d4-a809-bc5b4c7e4dd0/", "uuid": "13e27425-6a69-46d4-a809-bc5b4c7e4dd0", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIKJHNZTR/fastqc_report.html", "display_title": "QualityMetricFastqc from 2024-12-05", "Total Sequences": 1500127, "status": "released", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"@id": "/files-fastq/4DNFIKR3QSG2/", "file_type_detailed": "reads (fastq)", "accession": "4DNFIKR3QSG2", "status": "restricted", "uuid": "75d2f7ec-25e5-41a0-9472-3ed004dd8177", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "paired_end": "2", "display_title": "4DNFIKR3QSG2.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"relationship_type": "grouped with", "file": {"@id": "/files-fastq/4DNFIHRYZ9XG/", "file_type_detailed": "index reads (fastq)", "accession": "4DNFIHRYZ9XG", "status": "restricted", "uuid": "6fb253ac-05c4-44ca-bab0-ca31a214dfd1", "file_type": "index reads", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIHRYZ9XG.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"relationship_type": "grouped with", "file": {"@id": "/files-fastq/4DNFI9ZWA22P/", "file_type_detailed": "index reads (fastq)", "accession": "4DNFI9ZWA22P", "status": "restricted", "uuid": "ac476649-46ae-4c6b-8bea-7fc88e21317d", "file_type": "index reads", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFI9ZWA22P.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"file_type_detailed": "index reads (fastq)", "upload_key": "ac476649-46ae-4c6b-8bea-7fc88e21317d/4DNFI9ZWA22P.fastq.gz", "uuid": "ac476649-46ae-4c6b-8bea-7fc88e21317d", "accession": "4DNFI9ZWA22P", "display_title": "4DNFI9ZWA22P.fastq.gz", "@id": "/files-fastq/4DNFI9ZWA22P/", "@type": ["FileFastq", "File", "Item"], "status": "restricted", "file_size": 28254781, "file_classification": "raw file", "href": "/files-fastq/4DNFI9ZWA22P/@@download/4DNFI9ZWA22P.fastq.gz", "file_type": "index reads", "quality_metric": {"Sequence length": "16", "@id": "/quality-metrics-fastqc/ba95a0aa-d97c-4b53-8590-85aa1d2675b6/", "uuid": "ba95a0aa-d97c-4b53-8590-85aa1d2675b6", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI9ZWA22P/fastqc_report.html", "display_title": "QualityMetricFastqc from 2024-12-05", "Total Sequences": 1500127, "status": "released", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "grouped with", "file": {"@id": "/files-fastq/4DNFIKJHNZTR/", "file_type_detailed": "reads (fastq)", "accession": "4DNFIKJHNZTR", "status": "restricted", "uuid": "bdd093e2-3f38-4037-82f9-b2911a0d5474", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "paired_end": "1", "display_title": "4DNFIKJHNZTR.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"relationship_type": "grouped with", "file": {"@id": "/files-fastq/4DNFIKR3QSG2/", "file_type_detailed": "reads (fastq)", "accession": "4DNFIKR3QSG2", "status": "restricted", "uuid": "75d2f7ec-25e5-41a0-9472-3ed004dd8177", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "paired_end": "2", "display_title": "4DNFIKR3QSG2.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"file_type_detailed": "reads (fastq)", "upload_key": "75d2f7ec-25e5-41a0-9472-3ed004dd8177/4DNFIKR3QSG2.fastq.gz", "uuid": "75d2f7ec-25e5-41a0-9472-3ed004dd8177", "accession": "4DNFIKR3QSG2", "display_title": "4DNFIKR3QSG2.fastq.gz", "@id": "/files-fastq/4DNFIKR3QSG2/", "@type": ["FileFastq", "File", "Item"], "status": "restricted", "file_size": 54449887, "file_classification": "raw file", "href": "/files-fastq/4DNFIKR3QSG2/@@download/4DNFIKR3QSG2.fastq.gz", "file_type": "reads", "paired_end": "2", "quality_metric": {"Sequence length": "50", "@id": "/quality-metrics-fastqc/74c07e79-ddbc-46ec-9e29-e6f06480a0f1/", "uuid": "74c07e79-ddbc-46ec-9e29-e6f06480a0f1", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIKR3QSG2/fastqc_report.html", "display_title": "QualityMetricFastqc from 2024-12-05", "Total Sequences": 1500127, "status": "released", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"@id": "/files-fastq/4DNFIKJHNZTR/", "file_type_detailed": "reads (fastq)", "accession": "4DNFIKJHNZTR", "status": "restricted", "uuid": "bdd093e2-3f38-4037-82f9-b2911a0d5474", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "paired_end": "1", "display_title": "4DNFIKJHNZTR.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"relationship_type": "grouped with", "file": {"@id": "/files-fastq/4DNFIHRYZ9XG/", "file_type_detailed": "index reads (fastq)", "accession": "4DNFIHRYZ9XG", "status": "restricted", "uuid": "6fb253ac-05c4-44ca-bab0-ca31a214dfd1", "file_type": "index reads", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIHRYZ9XG.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"relationship_type": "grouped with", "file": {"@id": "/files-fastq/4DNFI9ZWA22P/", "file_type_detailed": "index reads (fastq)", "accession": "4DNFI9ZWA22P", "status": "restricted", "uuid": "ac476649-46ae-4c6b-8bea-7fc88e21317d", "file_type": "index reads", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFI9ZWA22P.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}], "status": "released", "aliases": ["bing-ren-lab:experiment_scATACseq_retina_donor_1"], "protocol": {"@id": "/protocols/4b2997a9-0f93-49f9-85a2-9e214d2d3ae0/", "@type": ["Protocol", "Item"], "uuid": "4b2997a9-0f93-49f9-85a2-9e214d2d3ae0", "display_title": "Experimental protocol", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNEX1O3VZ2N", "biosample": {"status": "released", "display_title": "4DNBSHA1RW53", "uuid": "f1f3c48c-e909-4e23-8953-225cc83730df", "biosource_summary": "retina", "@id": "/biosamples/4DNBSHA1RW53/", "modifications_summary": "None", "accession": "4DNBSHA1RW53", "@type": ["Biosample", "Item"], "biosample_type": "tissue", "treatments_summary": "None", "biosource": [{"lab": {"display_title": "4DN DCIC, HMS", "@id": "/labs/4dn-dcic-lab/", "@type": ["Lab", "Item"], "status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "award": {"status": "current", "uuid": "71171a4e-dca1-44cb-8375-fafd896c6923", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE II", "@id": "/awards/2U01CA200059-06/", "@type": ["Award", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "tissue": {"uuid": "b428a669-bee5-4a2a-9729-5cdfb372571a", "status": "released", "@id": "/ontology-terms/UBERON:0000966/", "@type": ["OntologyTerm", "Item"], "term_name": "retina", "term_id": "UBERON:0000966", "display_title": "retina", "preferred_name": "retina", "synonyms": ["tunica interna of eyeball", "inner layer of eyeball", "retina of camera-type eye"], "slim_terms": [{"display_title": "sensory system", "@id": "/ontology-terms/UBERON:0001032/", "status": "released", "uuid": "111135bc-8535-4448-903e-854af460a233", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "ectoderm", "@id": "/ontology-terms/UBERON:0000924/", "status": "released", "uuid": "111119bc-8535-4448-903e-854af460a233", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "eye", "@id": "/ontology-terms/UBERON:0000970/", "status": "released", "uuid": "111181bc-8535-4448-903e-854af460a233", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "aliases": ["bing-ren-lab:biosource_retina_donor_1"], "accession": "4DNSR1X8M3Z8", "individual": {"display_title": "4DNINKXWSZBM", "status": "released", "@id": "/individuals-human/4DNINKXWSZBM/", "uuid": "6c005c4b-7b7e-493d-8c87-cb9cfbb2d592", "@type": ["IndividualHuman", "Individual", "Item"], "protected_data": true, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "description": "Retina tissue from donor 1", "date_created": "2024-12-02T20:02:05.308899+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2025-06-10T15:58:44.180894+00:00"}, "biosource_type": "tissue", "cell_line_tier": "Unclassified", "public_release": "2025-06-10", "schema_version": "2", "project_release": "2025-06-10", "biosource_vendor": {"uuid": "fb595854-28f9-4e47-a0a3-0936fb3752b8", "display_title": "San Diego Eye Bank", "status": "released", "@type": ["Vendor", "Item"], "@id": "/vendors/san-diego-eye-bank/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@id": "/biosources/4DNSR1X8M3Z8/", "@type": ["Biosource", "Item"], "uuid": "9fa2fdd9-cb69-4d02-9970-b6a22532187d", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "retina - 4DNSR1X8M3Z8", "external_references": [], "biosource_name": "retina", "biosource_category": ["Multicellular Tissue"], "organism": {"status": "released", "@id": "/organisms/9606/", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "name": "human", "display_title": "H. sapiens", "@type": ["Organism", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "description": "Single cell ATAC-seq (scATACseq) in human eye, retina tissue from donor - 1, Biological replicate 1, Technical replicate 1", "sop_mapping": {"has_sop": "No"}, "date_created": "2024-12-02T20:41:21.170693+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2025-06-10T15:53:45.660837+00:00"}, "public_release": "2025-06-10", "schema_version": "2", "experiment_type": {"display_title": "single cell ATAC-seq", "assay_subclass_short": "Open Chromatin", "uuid": "a4bc3590-7298-480f-a1b0-697287a3df90", "status": "released", "title": "single cell ATAC-seq", "@type": ["ExperimentType", "Item"], "experiment_category": "Sequencing", "@id": "/experiment-types/single-cell-atac-seq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "project_release": "2025-06-10", "@id": "/experiments-atacseq/4DNEX1O3VZ2N/", "@type": ["ExperimentAtacseq", "Experiment", "Item"], "uuid": "b67aaef5-7b55-472e-95a7-2c4c4c3deec3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "single cell ATAC-seq on retina - 4DNEX1O3VZ2N", "external_references": [], "experiment_sets": [{"experimentset_type": "replicate", "@id": "/experiment-set-replicates/4DNESWCLFSO8/", "status": "released", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "accession": "4DNESWCLFSO8", "uuid": "d9dbd63d-62da-4608-8e38-dfadb752de7c", "display_title": "4DNESWCLFSO8", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "publications_of_exp": [], "experiment_categorizer": {"field": "Default", "value": null}, "experiment_summary": "single cell ATAC-seq on retina", "@context": "/terms/", "aggregated-items": {"badges": []}, "validation-errors": []}