{"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"]}}, "badges": [{"badge": {"badge_icon": "/static/img/badges/replicates-orange-circle.svg", "display_title": "Replicate Numbers", "title": "Replicate Numbers", "status": "released", "warning": "Replicate Numbers", "@id": "/badges/replicate-numbers/", "uuid": "24a64a84-3c33-4d76-aaf2-e5ef45eff347", "badge_classification": "Warning", "description": "Issues with replicate numbers", "@type": ["Badge", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "messages": ["Replicate set contains only a single biological replicate"]}], "status": "released", "aliases": ["bing-ren-lab:expset_scRNAseq_retina_mouse_donor1"], "accession": "4DNESN9LELPQ", "condition": "Donor 1 -  76 days old", "description": "Single cell RNA-seq (scRNAseq) in retina tissue from mouse (76 days old)  donor 1", "date_created": "2024-12-02T22:31:45.936528+00:00", "submitted_by": {"error": "no view permissions"}, "dataset_label": "scRNAseq in mouse eye tissue", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2025-06-23T19:11:56.928188+00:00"}, "public_release": "2025-06-10", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"status": "released", "display_title": "single cell RNA-seq on retina - 4DNEX3TUATIF", "@id": "/experiments-seq/4DNEX3TUATIF/", "@type": ["ExperimentSeq", "Experiment", "Item"], "accession": "4DNEX3TUATIF", "uuid": "6d2221ea-adc6-4710-b126-1aaf5b926097", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "static_headers": [{"lab": {"@type": ["Lab", "Item"], "status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "@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": {"status": "current", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "@id": "/awards/1U01CA200059-01/", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "@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": [{"display_title": "single cell RNA-seq on retina - 4DNEX3TUATIF", "@type": ["ExperimentSeq", "Experiment", "Item"], "accession": "4DNEX3TUATIF", "status": "released", "@id": "/experiments-seq/4DNEX3TUATIF/", "uuid": "6d2221ea-adc6-4710-b126-1aaf5b926097", "files": [{"uuid": "465700e0-b0c7-4cb1-8aaa-6990143a7913", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "index reads (fastq)", "file_classification": "raw file", "paired_end": "1", "status": "released", "upload_key": "465700e0-b0c7-4cb1-8aaa-6990143a7913/4DNFIVHIP824.fastq.gz", "href": "/files-fastq/4DNFIVHIP824/@@download/4DNFIVHIP824.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/465700e0-b0c7-4cb1-8aaa-6990143a7913/4DNFIVHIP824.fastq.gz", "accession": "4DNFIVHIP824", "md5sum": "dab6de290d6c0ee8754840e9bfd32d7d", "@id": "/files-fastq/4DNFIVHIP824/", "file_size": 5048023102, "display_title": "4DNFIVHIP824.fastq.gz", "file_type": "index reads", "related_files": [{"relationship_type": "paired with", "file": {"@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFI3AYEKK6/", "file_type_detailed": "reads (fastq)", "uuid": "207b9f35-c3cd-4109-bf13-1f76cf6a817e", "display_title": "4DNFI3AYEKK6.fastq.gz", "status": "released", "accession": "4DNFI3AYEKK6", "paired_end": "2", "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"Sequence length": "101", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIVHIP824/fastqc_report.html", "status": "released", "@id": "/quality-metrics-fastqc/3f34ba58-58ea-41db-be0e-9be6644a9a27/", "Total Sequences": 76347897, "uuid": "3f34ba58-58ea-41db-be0e-9be6644a9a27", "display_title": "QualityMetricFastqc from 2024-12-05", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "overall_quality_status": "PASS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@type": ["FileFormat", "Item"], "display_title": "fastq", "status": "released", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "status": "current", "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"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Bing Ren, UCSD", "experiment_type": "single cell RNA-seq", "experiment_bucket": "raw file", "dataset": "scRNAseq in mouse eye tissue", "condition": "Donor 1 -  76 days old", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "retina", "lab_name": "Bing Ren, UCSD"}, "external_references": []}, {"uuid": "207b9f35-c3cd-4109-bf13-1f76cf6a817e", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "file_classification": "raw file", "paired_end": "2", "status": "released", "upload_key": "207b9f35-c3cd-4109-bf13-1f76cf6a817e/4DNFI3AYEKK6.fastq.gz", "href": "/files-fastq/4DNFI3AYEKK6/@@download/4DNFI3AYEKK6.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/207b9f35-c3cd-4109-bf13-1f76cf6a817e/4DNFI3AYEKK6.fastq.gz", "accession": "4DNFI3AYEKK6", "md5sum": "5b4333b5f683dcfa9c7865f6be4fb9b5", "@id": "/files-fastq/4DNFI3AYEKK6/", "file_size": 4224351019, "display_title": "4DNFI3AYEKK6.fastq.gz", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIVHIP824/", "file_type_detailed": "index reads (fastq)", "uuid": "465700e0-b0c7-4cb1-8aaa-6990143a7913", "display_title": "4DNFIVHIP824.fastq.gz", "status": "released", "accession": "4DNFIVHIP824", "paired_end": "1", "file_type": "index reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"Sequence length": "101", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI3AYEKK6/fastqc_report.html", "status": "released", "@id": "/quality-metrics-fastqc/c48c0ae1-fe63-4a0b-a036-f3bfc8f75cc0/", "Total Sequences": 76347897, "uuid": "c48c0ae1-fe63-4a0b-a036-f3bfc8f75cc0", "display_title": "QualityMetricFastqc from 2024-12-05", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "overall_quality_status": "PASS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@type": ["FileFormat", "Item"], "display_title": "fastq", "status": "released", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "status": "current", "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"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Bing Ren, UCSD", "experiment_type": "single cell RNA-seq", "experiment_bucket": "raw file", "dataset": "scRNAseq in mouse eye tissue", "condition": "Donor 1 -  76 days old", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "retina", "lab_name": "Bing Ren, UCSD"}, "external_references": []}, {"uuid": "71f8a7ad-a26e-481a-87b9-5162197d6190", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "file_classification": "raw file", "paired_end": "1", "status": "released", "upload_key": "71f8a7ad-a26e-481a-87b9-5162197d6190/4DNFI9TOLPUL.fastq.gz", "href": "/files-fastq/4DNFI9TOLPUL/@@download/4DNFI9TOLPUL.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/71f8a7ad-a26e-481a-87b9-5162197d6190/4DNFI9TOLPUL.fastq.gz", "accession": "4DNFI9TOLPUL", "md5sum": "dd9be388005c8bca278725ea479f45bc", "@id": "/files-fastq/4DNFI9TOLPUL/", "file_size": 5057788979, "display_title": "4DNFI9TOLPUL.fastq.gz", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIEM4JPSX/", "file_type_detailed": "reads (fastq)", "uuid": "6168442b-2993-4912-b400-f7f9d789743c", "display_title": "4DNFIEM4JPSX.fastq.gz", "status": "released", "accession": "4DNFIEM4JPSX", "paired_end": "2", "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"Sequence length": "101", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI9TOLPUL/fastqc_report.html", "status": "released", "@id": "/quality-metrics-fastqc/1f74bc1d-664c-41c5-8327-183ea3a120d3/", "Total Sequences": 76563598, "uuid": "1f74bc1d-664c-41c5-8327-183ea3a120d3", "display_title": "QualityMetricFastqc from 2024-12-05", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "overall_quality_status": "PASS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@type": ["FileFormat", "Item"], "display_title": "fastq", "status": "released", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "status": "current", "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"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Bing Ren, UCSD", "experiment_type": "single cell RNA-seq", "experiment_bucket": "raw file", "dataset": "scRNAseq in mouse eye tissue", "condition": "Donor 1 -  76 days old", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "retina", "lab_name": "Bing Ren, UCSD"}, "external_references": []}, {"uuid": "6168442b-2993-4912-b400-f7f9d789743c", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "file_classification": "raw file", "paired_end": "2", "status": "released", "upload_key": "6168442b-2993-4912-b400-f7f9d789743c/4DNFIEM4JPSX.fastq.gz", "href": "/files-fastq/4DNFIEM4JPSX/@@download/4DNFIEM4JPSX.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/6168442b-2993-4912-b400-f7f9d789743c/4DNFIEM4JPSX.fastq.gz", "accession": "4DNFIEM4JPSX", "md5sum": "0c60112af79c89a8eff397619f701532", "@id": "/files-fastq/4DNFIEM4JPSX/", "file_size": 4216669485, "display_title": "4DNFIEM4JPSX.fastq.gz", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFI9TOLPUL/", "file_type_detailed": "reads (fastq)", "uuid": "71f8a7ad-a26e-481a-87b9-5162197d6190", "display_title": "4DNFI9TOLPUL.fastq.gz", "status": "released", "accession": "4DNFI9TOLPUL", "paired_end": "1", "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"Sequence length": "101", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIEM4JPSX/fastqc_report.html", "status": "released", "@id": "/quality-metrics-fastqc/d390edb5-5f62-49b9-8942-675cb1feb934/", "Total Sequences": 76563598, "uuid": "d390edb5-5f62-49b9-8942-675cb1feb934", "display_title": "QualityMetricFastqc from 2024-12-05", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "overall_quality_status": "PASS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@type": ["FileFormat", "Item"], "display_title": "fastq", "status": "released", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "status": "current", "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"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Bing Ren, UCSD", "experiment_type": "single cell RNA-seq", "experiment_bucket": "raw file", "dataset": "scRNAseq in mouse eye tissue", "condition": "Donor 1 -  76 days old", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "retina", "lab_name": "Bing Ren, UCSD"}, "external_references": []}, {"uuid": "cb6a6fa1-0f56-46a0-91c6-eff2e9df2f7b", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "index reads (fastq)", "file_classification": "raw file", "status": "released", "upload_key": "cb6a6fa1-0f56-46a0-91c6-eff2e9df2f7b/4DNFIFOENMKA.fastq.gz", "href": "/files-fastq/4DNFIFOENMKA/@@download/4DNFIFOENMKA.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/cb6a6fa1-0f56-46a0-91c6-eff2e9df2f7b/4DNFIFOENMKA.fastq.gz", "accession": "4DNFIFOENMKA", "md5sum": "cf3f69271629eb686c288e887fd2517d", "@id": "/files-fastq/4DNFIFOENMKA/", "file_size": 25917471, "display_title": "4DNFIFOENMKA.fastq.gz", "file_type": "index reads", "related_files": [{"relationship_type": "grouped with", "file": {"@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFI4PUEJCE/", "file_type_detailed": "reads (fastq)", "uuid": "f79f90bf-2266-4ed1-890e-a8b523695beb", "display_title": "4DNFI4PUEJCE.fastq.gz", "status": "released", "accession": "4DNFI4PUEJCE", "paired_end": "1", "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"relationship_type": "grouped with", "file": {"@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIDHGNFJM/", "file_type_detailed": "reads (fastq)", "uuid": "3633e382-32c0-4c09-bed6-a2980037f69b", "display_title": "4DNFIDHGNFJM.fastq.gz", "status": "released", "accession": "4DNFIDHGNFJM", "paired_end": "2", "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"Sequence length": "10", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIFOENMKA/fastqc_report.html", "status": "released", "@id": "/quality-metrics-fastqc/097857b1-d65f-4534-bc73-9c0a71e763ac/", "Total Sequences": 3090747, "uuid": "097857b1-d65f-4534-bc73-9c0a71e763ac", "display_title": "QualityMetricFastqc from 2024-12-05", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "overall_quality_status": "PASS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@type": ["FileFormat", "Item"], "display_title": "fastq", "status": "released", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "status": "current", "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"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Bing Ren, UCSD", "experiment_type": "single cell RNA-seq", "experiment_bucket": "raw file", "dataset": "scRNAseq in mouse eye tissue", "condition": "Donor 1 -  76 days old", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "retina", "lab_name": "Bing Ren, UCSD"}, "external_references": []}, {"uuid": "39122409-bb72-4365-b505-40b15f09684e", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "index reads (fastq)", "file_classification": "raw file", "status": "released", "upload_key": "39122409-bb72-4365-b505-40b15f09684e/4DNFICH6WXVN.fastq.gz", "href": "/files-fastq/4DNFICH6WXVN/@@download/4DNFICH6WXVN.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/39122409-bb72-4365-b505-40b15f09684e/4DNFICH6WXVN.fastq.gz", "accession": "4DNFICH6WXVN", "md5sum": "a07b8a00a55cd25b70f564f7e4dc14b0", "@id": "/files-fastq/4DNFICH6WXVN/", "file_size": 28413505, "display_title": "4DNFICH6WXVN.fastq.gz", "file_type": "index reads", "related_files": [{"relationship_type": "grouped with", "file": {"@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFI4PUEJCE/", "file_type_detailed": "reads (fastq)", "uuid": "f79f90bf-2266-4ed1-890e-a8b523695beb", "display_title": "4DNFI4PUEJCE.fastq.gz", "status": "released", "accession": "4DNFI4PUEJCE", "paired_end": "1", "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"relationship_type": "grouped with", "file": {"@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIDHGNFJM/", "file_type_detailed": "reads (fastq)", "uuid": "3633e382-32c0-4c09-bed6-a2980037f69b", "display_title": "4DNFIDHGNFJM.fastq.gz", "status": "released", "accession": "4DNFIDHGNFJM", "paired_end": "2", "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"Sequence length": "10", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFICH6WXVN/fastqc_report.html", "status": "released", "@id": "/quality-metrics-fastqc/854e5f31-7129-439c-b4a8-34188c6d8145/", "Total Sequences": 3090747, "uuid": "854e5f31-7129-439c-b4a8-34188c6d8145", "display_title": "QualityMetricFastqc from 2024-12-05", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "overall_quality_status": "PASS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@type": ["FileFormat", "Item"], "display_title": "fastq", "status": "released", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "status": "current", "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"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Bing Ren, UCSD", "experiment_type": "single cell RNA-seq", "experiment_bucket": "raw file", "dataset": "scRNAseq in mouse eye tissue", "condition": "Donor 1 -  76 days old", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "retina", "lab_name": "Bing Ren, UCSD"}, "external_references": []}, {"uuid": "f79f90bf-2266-4ed1-890e-a8b523695beb", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "file_classification": "raw file", "paired_end": "1", "status": "released", "upload_key": "f79f90bf-2266-4ed1-890e-a8b523695beb/4DNFI4PUEJCE.fastq.gz", "href": "/files-fastq/4DNFI4PUEJCE/@@download/4DNFI4PUEJCE.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/f79f90bf-2266-4ed1-890e-a8b523695beb/4DNFI4PUEJCE.fastq.gz", "accession": "4DNFI4PUEJCE", "md5sum": "e0465ff09851d677ef9ca103ec7dc68e", "@id": "/files-fastq/4DNFI4PUEJCE/", "file_size": 73747210, "display_title": "4DNFI4PUEJCE.fastq.gz", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIDHGNFJM/", "file_type_detailed": "reads (fastq)", "uuid": "3633e382-32c0-4c09-bed6-a2980037f69b", "display_title": "4DNFIDHGNFJM.fastq.gz", "status": "released", "accession": "4DNFIDHGNFJM", "paired_end": "2", "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"relationship_type": "grouped with", "file": {"@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIFOENMKA/", "file_type_detailed": "index reads (fastq)", "uuid": "cb6a6fa1-0f56-46a0-91c6-eff2e9df2f7b", "display_title": "4DNFIFOENMKA.fastq.gz", "status": "released", "accession": "4DNFIFOENMKA", "file_type": "index reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"relationship_type": "grouped with", "file": {"@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFICH6WXVN/", "file_type_detailed": "index reads (fastq)", "uuid": "39122409-bb72-4365-b505-40b15f09684e", "display_title": "4DNFICH6WXVN.fastq.gz", "status": "released", "accession": "4DNFICH6WXVN", "file_type": "index reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"Sequence length": "28", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI4PUEJCE/fastqc_report.html", "status": "released", "@id": "/quality-metrics-fastqc/3a45155e-58d8-43f5-bd67-194b35cb48d1/", "Total Sequences": 3090747, "uuid": "3a45155e-58d8-43f5-bd67-194b35cb48d1", "display_title": "QualityMetricFastqc from 2024-12-05", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "overall_quality_status": "PASS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@type": ["FileFormat", "Item"], "display_title": "fastq", "status": "released", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "status": "current", "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"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Bing Ren, UCSD", "experiment_type": "single cell RNA-seq", "experiment_bucket": "raw file", "dataset": "scRNAseq in mouse eye tissue", "condition": "Donor 1 -  76 days old", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "retina", "lab_name": "Bing Ren, UCSD"}, "external_references": []}, {"uuid": "3633e382-32c0-4c09-bed6-a2980037f69b", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "file_classification": "raw file", "paired_end": "2", "status": "released", "upload_key": "3633e382-32c0-4c09-bed6-a2980037f69b/4DNFIDHGNFJM.fastq.gz", "href": "/files-fastq/4DNFIDHGNFJM/@@download/4DNFIDHGNFJM.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/3633e382-32c0-4c09-bed6-a2980037f69b/4DNFIDHGNFJM.fastq.gz", "accession": "4DNFIDHGNFJM", "md5sum": "c61f00db11d73836f152ea28ac78ccf7", "@id": "/files-fastq/4DNFIDHGNFJM/", "file_size": 175100780, "display_title": "4DNFIDHGNFJM.fastq.gz", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFI4PUEJCE/", "file_type_detailed": "reads (fastq)", "uuid": "f79f90bf-2266-4ed1-890e-a8b523695beb", "display_title": "4DNFI4PUEJCE.fastq.gz", "status": "released", "accession": "4DNFI4PUEJCE", "paired_end": "1", "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"relationship_type": "grouped with", "file": {"@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIFOENMKA/", "file_type_detailed": "index reads (fastq)", "uuid": "cb6a6fa1-0f56-46a0-91c6-eff2e9df2f7b", "display_title": "4DNFIFOENMKA.fastq.gz", "status": "released", "accession": "4DNFIFOENMKA", "file_type": "index reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"relationship_type": "grouped with", "file": {"@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFICH6WXVN/", "file_type_detailed": "index reads (fastq)", "uuid": "39122409-bb72-4365-b505-40b15f09684e", "display_title": "4DNFICH6WXVN.fastq.gz", "status": "released", "accession": "4DNFICH6WXVN", "file_type": "index reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"Sequence length": "91", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIDHGNFJM/fastqc_report.html", "status": "released", "@id": "/quality-metrics-fastqc/6d32b594-9398-4439-ab7d-faab614f8eff/", "Total Sequences": 3090747, "uuid": "6d32b594-9398-4439-ab7d-faab614f8eff", "display_title": "QualityMetricFastqc from 2024-12-05", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "overall_quality_status": "PASS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@type": ["FileFormat", "Item"], "display_title": "fastq", "status": "released", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "status": "current", "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"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Bing Ren, UCSD", "experiment_type": "single cell RNA-seq", "experiment_bucket": "raw file", "dataset": "scRNAseq in mouse eye tissue", "condition": "Donor 1 -  76 days old", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "retina", "lab_name": "Bing Ren, UCSD"}, "external_references": []}, {"uuid": "9790e4a6-7f1d-43bd-83f6-7a9254fc6274", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "index reads (fastq)", "file_classification": "raw file", "status": "released", "upload_key": "9790e4a6-7f1d-43bd-83f6-7a9254fc6274/4DNFIAPZBTM8.fastq.gz", "href": "/files-fastq/4DNFIAPZBTM8/@@download/4DNFIAPZBTM8.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/9790e4a6-7f1d-43bd-83f6-7a9254fc6274/4DNFIAPZBTM8.fastq.gz", "accession": "4DNFIAPZBTM8", "md5sum": "15f3511b3e9b002dd61bbda54a297d05", "@id": "/files-fastq/4DNFIAPZBTM8/", "file_size": 25341425, "display_title": "4DNFIAPZBTM8.fastq.gz", "file_type": "index reads", "related_files": [{"relationship_type": "grouped with", "file": {"@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIF6YG3ED/", "file_type_detailed": "reads (fastq)", "uuid": "6925a4a7-ba42-4683-9be7-d31341efcfd8", "display_title": "4DNFIF6YG3ED.fastq.gz", "status": "released", "accession": "4DNFIF6YG3ED", "paired_end": "1", "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"relationship_type": "grouped with", "file": {"@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIR9B17NT/", "file_type_detailed": "reads (fastq)", "uuid": "7fe5503e-8c3b-414f-8539-f1ba1c48424d", "display_title": "4DNFIR9B17NT.fastq.gz", "status": "released", "accession": "4DNFIR9B17NT", "paired_end": "2", "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"Sequence length": "10", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIAPZBTM8/fastqc_report.html", "status": "released", "@id": "/quality-metrics-fastqc/67f85d41-61eb-4e0a-a848-11eb28fa4727/", "Total Sequences": 3031746, "uuid": "67f85d41-61eb-4e0a-a848-11eb28fa4727", "display_title": "QualityMetricFastqc from 2024-12-05", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "overall_quality_status": "PASS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@type": ["FileFormat", "Item"], "display_title": "fastq", "status": "released", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "status": "current", "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"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Bing Ren, UCSD", "experiment_type": "single cell RNA-seq", "experiment_bucket": "raw file", "dataset": "scRNAseq in mouse eye tissue", "condition": "Donor 1 -  76 days old", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "retina", "lab_name": "Bing Ren, UCSD"}, "external_references": []}, {"uuid": "49d91f60-98ad-4da1-9a46-d2b9c509e55e", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "index reads (fastq)", "file_classification": "raw file", "status": "released", "upload_key": "49d91f60-98ad-4da1-9a46-d2b9c509e55e/4DNFIZWG5C5X.fastq.gz", "href": "/files-fastq/4DNFIZWG5C5X/@@download/4DNFIZWG5C5X.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/49d91f60-98ad-4da1-9a46-d2b9c509e55e/4DNFIZWG5C5X.fastq.gz", "accession": "4DNFIZWG5C5X", "md5sum": "3d5496aa01b8b8f88a3fdd98add1c328", "@id": "/files-fastq/4DNFIZWG5C5X/", "file_size": 27707563, "display_title": "4DNFIZWG5C5X.fastq.gz", "file_type": "index reads", "related_files": [{"relationship_type": "grouped with", "file": {"@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIF6YG3ED/", "file_type_detailed": "reads (fastq)", "uuid": "6925a4a7-ba42-4683-9be7-d31341efcfd8", "display_title": "4DNFIF6YG3ED.fastq.gz", "status": "released", "accession": "4DNFIF6YG3ED", "paired_end": "1", "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"relationship_type": "grouped with", "file": {"@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIR9B17NT/", "file_type_detailed": "reads (fastq)", "uuid": "7fe5503e-8c3b-414f-8539-f1ba1c48424d", "display_title": "4DNFIR9B17NT.fastq.gz", "status": "released", "accession": "4DNFIR9B17NT", "paired_end": "2", "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"Sequence length": "10", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIZWG5C5X/fastqc_report.html", "status": "released", "@id": "/quality-metrics-fastqc/a9dd89d1-ebde-4ae9-a592-1b432a186f76/", "Total Sequences": 3031746, "uuid": "a9dd89d1-ebde-4ae9-a592-1b432a186f76", "display_title": "QualityMetricFastqc from 2024-12-05", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "overall_quality_status": "PASS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@type": ["FileFormat", "Item"], "display_title": "fastq", "status": "released", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "status": "current", "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"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Bing Ren, UCSD", "experiment_type": "single cell RNA-seq", "experiment_bucket": "raw file", "dataset": "scRNAseq in mouse eye tissue", "condition": "Donor 1 -  76 days old", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "retina", "lab_name": "Bing Ren, UCSD"}, "external_references": []}, {"uuid": "6925a4a7-ba42-4683-9be7-d31341efcfd8", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "file_classification": "raw file", "paired_end": "1", "status": "released", "upload_key": "6925a4a7-ba42-4683-9be7-d31341efcfd8/4DNFIF6YG3ED.fastq.gz", "href": "/files-fastq/4DNFIF6YG3ED/@@download/4DNFIF6YG3ED.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/6925a4a7-ba42-4683-9be7-d31341efcfd8/4DNFIF6YG3ED.fastq.gz", "accession": "4DNFIF6YG3ED", "md5sum": "89d4539d2e8168c39593abd133032bdf", "@id": "/files-fastq/4DNFIF6YG3ED/", "file_size": 71980789, "display_title": "4DNFIF6YG3ED.fastq.gz", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIR9B17NT/", "file_type_detailed": "reads (fastq)", "uuid": "7fe5503e-8c3b-414f-8539-f1ba1c48424d", "display_title": "4DNFIR9B17NT.fastq.gz", "status": "released", "accession": "4DNFIR9B17NT", "paired_end": "2", "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"relationship_type": "grouped with", "file": {"@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIAPZBTM8/", "file_type_detailed": "index reads (fastq)", "uuid": "9790e4a6-7f1d-43bd-83f6-7a9254fc6274", "display_title": "4DNFIAPZBTM8.fastq.gz", "status": "released", "accession": "4DNFIAPZBTM8", "file_type": "index reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"relationship_type": "grouped with", "file": {"@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIZWG5C5X/", "file_type_detailed": "index reads (fastq)", "uuid": "49d91f60-98ad-4da1-9a46-d2b9c509e55e", "display_title": "4DNFIZWG5C5X.fastq.gz", "status": "released", "accession": "4DNFIZWG5C5X", "file_type": "index reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"Sequence length": "28", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIF6YG3ED/fastqc_report.html", "status": "released", "@id": "/quality-metrics-fastqc/8086ea6e-25b7-4281-a58d-242be116bce8/", "Total Sequences": 3031746, "uuid": "8086ea6e-25b7-4281-a58d-242be116bce8", "display_title": "QualityMetricFastqc from 2024-12-05", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "overall_quality_status": "PASS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@type": ["FileFormat", "Item"], "display_title": "fastq", "status": "released", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "status": "current", "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"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Bing Ren, UCSD", "experiment_type": "single cell RNA-seq", "experiment_bucket": "raw file", "dataset": "scRNAseq in mouse eye tissue", "condition": "Donor 1 -  76 days old", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "retina", "lab_name": "Bing Ren, UCSD"}, "external_references": []}, {"uuid": "7fe5503e-8c3b-414f-8539-f1ba1c48424d", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "file_classification": "raw file", "paired_end": "2", "status": "released", "upload_key": "7fe5503e-8c3b-414f-8539-f1ba1c48424d/4DNFIR9B17NT.fastq.gz", "href": "/files-fastq/4DNFIR9B17NT/@@download/4DNFIR9B17NT.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/7fe5503e-8c3b-414f-8539-f1ba1c48424d/4DNFIR9B17NT.fastq.gz", "accession": "4DNFIR9B17NT", "md5sum": "6a30a7fb2a67c9101b60320786826224", "@id": "/files-fastq/4DNFIR9B17NT/", "file_size": 170111425, "display_title": "4DNFIR9B17NT.fastq.gz", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIF6YG3ED/", "file_type_detailed": "reads (fastq)", "uuid": "6925a4a7-ba42-4683-9be7-d31341efcfd8", "display_title": "4DNFIF6YG3ED.fastq.gz", "status": "released", "accession": "4DNFIF6YG3ED", "paired_end": "1", "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"relationship_type": "grouped with", "file": {"@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIAPZBTM8/", "file_type_detailed": "index reads (fastq)", "uuid": "9790e4a6-7f1d-43bd-83f6-7a9254fc6274", "display_title": "4DNFIAPZBTM8.fastq.gz", "status": "released", "accession": "4DNFIAPZBTM8", "file_type": "index reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"relationship_type": "grouped with", "file": {"@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIZWG5C5X/", "file_type_detailed": "index reads (fastq)", "uuid": "49d91f60-98ad-4da1-9a46-d2b9c509e55e", "display_title": "4DNFIZWG5C5X.fastq.gz", "status": "released", "accession": "4DNFIZWG5C5X", "file_type": "index reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"Sequence length": "91", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIR9B17NT/fastqc_report.html", "status": "released", "@id": "/quality-metrics-fastqc/4d1b8ba3-c369-4cff-82b0-47353f8dc2b2/", "Total Sequences": 3031746, "uuid": "4d1b8ba3-c369-4cff-82b0-47353f8dc2b2", "display_title": "QualityMetricFastqc from 2024-12-05", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "overall_quality_status": "PASS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@type": ["FileFormat", "Item"], "display_title": "fastq", "status": "released", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "status": "current", "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"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Bing Ren, UCSD", "experiment_type": "single cell RNA-seq", "experiment_bucket": "raw file", "dataset": "scRNAseq in mouse eye tissue", "condition": "Donor 1 -  76 days old", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "retina", "lab_name": "Bing Ren, UCSD"}, "external_references": []}, {"uuid": "b174268d-8de7-459b-9b61-13284196bb2c", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "index reads (fastq)", "file_classification": "raw file", "status": "released", "upload_key": "b174268d-8de7-459b-9b61-13284196bb2c/4DNFIHSIIZG6.fastq.gz", "href": "/files-fastq/4DNFIHSIIZG6/@@download/4DNFIHSIIZG6.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/b174268d-8de7-459b-9b61-13284196bb2c/4DNFIHSIIZG6.fastq.gz", "accession": "4DNFIHSIIZG6", "md5sum": "7c773112ffc07dd7190e27d1d188d07e", "@id": "/files-fastq/4DNFIHSIIZG6/", "file_size": 26215415, "display_title": "4DNFIHSIIZG6.fastq.gz", "file_type": "index reads", "related_files": [{"relationship_type": "grouped with", "file": {"@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIVTLBRT4/", "file_type_detailed": "reads (fastq)", "uuid": "ea69820e-9749-4df2-9ff9-798367b91482", "display_title": "4DNFIVTLBRT4.fastq.gz", "status": "released", "accession": "4DNFIVTLBRT4", "paired_end": "1", "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"relationship_type": "grouped with", "file": {"@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIU6Y1DAN/", "file_type_detailed": "reads (fastq)", "uuid": "c0e11cff-8c03-478b-ab62-992959dc8870", "display_title": "4DNFIU6Y1DAN.fastq.gz", "status": "released", "accession": "4DNFIU6Y1DAN", "paired_end": "2", "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"Sequence length": "10", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIHSIIZG6/fastqc_report.html", "status": "released", "@id": "/quality-metrics-fastqc/b8b97664-5f83-40f1-9879-a84ea9e70ebb/", "Total Sequences": 3127002, "uuid": "b8b97664-5f83-40f1-9879-a84ea9e70ebb", "display_title": "QualityMetricFastqc from 2024-12-05", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "overall_quality_status": "PASS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@type": ["FileFormat", "Item"], "display_title": "fastq", "status": "released", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "status": "current", "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"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Bing Ren, UCSD", "experiment_type": "single cell RNA-seq", "experiment_bucket": "raw file", "dataset": "scRNAseq in mouse eye tissue", "condition": "Donor 1 -  76 days old", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "retina", "lab_name": "Bing Ren, UCSD"}, "external_references": []}, {"uuid": "325aebc9-37fa-4495-8f32-529d215128d0", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "index reads (fastq)", "file_classification": "raw file", "status": "released", "upload_key": "325aebc9-37fa-4495-8f32-529d215128d0/4DNFIDPKPF5C.fastq.gz", "href": "/files-fastq/4DNFIDPKPF5C/@@download/4DNFIDPKPF5C.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/325aebc9-37fa-4495-8f32-529d215128d0/4DNFIDPKPF5C.fastq.gz", "accession": "4DNFIDPKPF5C", "md5sum": "46a4eaabb27da13640b79bb4ba7954fa", "@id": "/files-fastq/4DNFIDPKPF5C/", "file_size": 28821275, "display_title": "4DNFIDPKPF5C.fastq.gz", "file_type": "index reads", "related_files": [{"relationship_type": "grouped with", "file": {"@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIVTLBRT4/", "file_type_detailed": "reads (fastq)", "uuid": "ea69820e-9749-4df2-9ff9-798367b91482", "display_title": "4DNFIVTLBRT4.fastq.gz", "status": "released", "accession": "4DNFIVTLBRT4", "paired_end": "1", "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"relationship_type": "grouped with", "file": {"@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIU6Y1DAN/", "file_type_detailed": "reads (fastq)", "uuid": "c0e11cff-8c03-478b-ab62-992959dc8870", "display_title": "4DNFIU6Y1DAN.fastq.gz", "status": "released", "accession": "4DNFIU6Y1DAN", "paired_end": "2", "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"Sequence length": "10", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIDPKPF5C/fastqc_report.html", "status": "released", "@id": "/quality-metrics-fastqc/55d5aabf-1ae6-4c47-9d0d-0fc3d9d745f7/", "Total Sequences": 3127002, "uuid": "55d5aabf-1ae6-4c47-9d0d-0fc3d9d745f7", "display_title": "QualityMetricFastqc from 2024-12-05", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "overall_quality_status": "PASS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@type": ["FileFormat", "Item"], "display_title": "fastq", "status": "released", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "status": "current", "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"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Bing Ren, UCSD", "experiment_type": "single cell RNA-seq", "experiment_bucket": "raw file", "dataset": "scRNAseq in mouse eye tissue", "condition": "Donor 1 -  76 days old", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "retina", "lab_name": "Bing Ren, UCSD"}, "external_references": []}, {"uuid": "ea69820e-9749-4df2-9ff9-798367b91482", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "file_classification": "raw file", "paired_end": "1", "status": "released", "upload_key": "ea69820e-9749-4df2-9ff9-798367b91482/4DNFIVTLBRT4.fastq.gz", "href": "/files-fastq/4DNFIVTLBRT4/@@download/4DNFIVTLBRT4.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/ea69820e-9749-4df2-9ff9-798367b91482/4DNFIVTLBRT4.fastq.gz", "accession": "4DNFIVTLBRT4", "md5sum": "0e1ac931f0b7eba29ad2350bcae2a564", "@id": "/files-fastq/4DNFIVTLBRT4/", "file_size": 74519986, "display_title": "4DNFIVTLBRT4.fastq.gz", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIU6Y1DAN/", "file_type_detailed": "reads (fastq)", "uuid": "c0e11cff-8c03-478b-ab62-992959dc8870", "display_title": "4DNFIU6Y1DAN.fastq.gz", "status": "released", "accession": "4DNFIU6Y1DAN", "paired_end": "2", "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"relationship_type": "grouped with", "file": {"@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIHSIIZG6/", "file_type_detailed": "index reads (fastq)", "uuid": "b174268d-8de7-459b-9b61-13284196bb2c", "display_title": "4DNFIHSIIZG6.fastq.gz", "status": "released", "accession": "4DNFIHSIIZG6", "file_type": "index reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"relationship_type": "grouped with", "file": {"@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIDPKPF5C/", "file_type_detailed": "index reads (fastq)", "uuid": "325aebc9-37fa-4495-8f32-529d215128d0", "display_title": "4DNFIDPKPF5C.fastq.gz", "status": "released", "accession": "4DNFIDPKPF5C", "file_type": "index reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"Sequence length": "28", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIVTLBRT4/fastqc_report.html", "status": "released", "@id": "/quality-metrics-fastqc/1121276d-6dfb-4ddf-9255-777bad745388/", "Total Sequences": 3127002, "uuid": "1121276d-6dfb-4ddf-9255-777bad745388", "display_title": "QualityMetricFastqc from 2024-12-05", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "overall_quality_status": "PASS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@type": ["FileFormat", "Item"], "display_title": "fastq", "status": "released", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "status": "current", "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"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Bing Ren, UCSD", "experiment_type": "single cell RNA-seq", "experiment_bucket": "raw file", "dataset": "scRNAseq in mouse eye tissue", "condition": "Donor 1 -  76 days old", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "retina", "lab_name": "Bing Ren, UCSD"}, "external_references": []}, {"uuid": "c0e11cff-8c03-478b-ab62-992959dc8870", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "file_classification": "raw file", "paired_end": "2", "status": "released", "upload_key": "c0e11cff-8c03-478b-ab62-992959dc8870/4DNFIU6Y1DAN.fastq.gz", "href": "/files-fastq/4DNFIU6Y1DAN/@@download/4DNFIU6Y1DAN.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/c0e11cff-8c03-478b-ab62-992959dc8870/4DNFIU6Y1DAN.fastq.gz", "accession": "4DNFIU6Y1DAN", "md5sum": "a90f98c25aae3fffbcb338b9cf6febee", "@id": "/files-fastq/4DNFIU6Y1DAN/", "file_size": 177203893, "display_title": "4DNFIU6Y1DAN.fastq.gz", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIVTLBRT4/", "file_type_detailed": "reads (fastq)", "uuid": "ea69820e-9749-4df2-9ff9-798367b91482", "display_title": "4DNFIVTLBRT4.fastq.gz", "status": "released", "accession": "4DNFIVTLBRT4", "paired_end": "1", "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"relationship_type": "grouped with", "file": {"@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIHSIIZG6/", "file_type_detailed": "index reads (fastq)", "uuid": "b174268d-8de7-459b-9b61-13284196bb2c", "display_title": "4DNFIHSIIZG6.fastq.gz", "status": "released", "accession": "4DNFIHSIIZG6", "file_type": "index reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"relationship_type": "grouped with", "file": {"@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIDPKPF5C/", "file_type_detailed": "index reads (fastq)", "uuid": "325aebc9-37fa-4495-8f32-529d215128d0", "display_title": "4DNFIDPKPF5C.fastq.gz", "status": "released", "accession": "4DNFIDPKPF5C", "file_type": "index reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"Sequence length": "91", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIU6Y1DAN/fastqc_report.html", "status": "released", "@id": "/quality-metrics-fastqc/57856960-3f1e-485b-b344-e7754dcfb62a/", "Total Sequences": 3127002, "uuid": "57856960-3f1e-485b-b344-e7754dcfb62a", "display_title": "QualityMetricFastqc from 2024-12-05", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "overall_quality_status": "PASS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@type": ["FileFormat", "Item"], "display_title": "fastq", "status": "released", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "status": "current", "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"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Bing Ren, UCSD", "experiment_type": "single cell RNA-seq", "experiment_bucket": "raw file", "dataset": "scRNAseq in mouse eye tissue", "condition": "Donor 1 -  76 days old", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "retina", "lab_name": "Bing Ren, UCSD"}, "external_references": []}, {"uuid": "7993b152-fbb6-4c7f-9d5c-797c6b14b4e3", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "index reads (fastq)", "file_classification": "raw file", "status": "released", "upload_key": "7993b152-fbb6-4c7f-9d5c-797c6b14b4e3/4DNFIISKNNHN.fastq.gz", "href": "/files-fastq/4DNFIISKNNHN/@@download/4DNFIISKNNHN.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/7993b152-fbb6-4c7f-9d5c-797c6b14b4e3/4DNFIISKNNHN.fastq.gz", "accession": "4DNFIISKNNHN", "md5sum": "5d4bcb57b9ef27c7ab94af8cc73adab6", "@id": "/files-fastq/4DNFIISKNNHN/", "file_size": 25592866, "display_title": "4DNFIISKNNHN.fastq.gz", "file_type": "index reads", "related_files": [{"relationship_type": "grouped with", "file": {"@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIYD6DB85/", "file_type_detailed": "reads (fastq)", "uuid": "1e4597a4-b0f0-475e-8a2a-409860ec700b", "display_title": "4DNFIYD6DB85.fastq.gz", "status": "released", "accession": "4DNFIYD6DB85", "paired_end": "1", "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"relationship_type": "grouped with", "file": {"@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFI21PLQYB/", "file_type_detailed": "reads (fastq)", "uuid": "53a8e48a-f878-4997-bffd-3dcffcecbaa3", "display_title": "4DNFI21PLQYB.fastq.gz", "status": "released", "accession": "4DNFI21PLQYB", "paired_end": "2", "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"Sequence length": "10", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIISKNNHN/fastqc_report.html", "status": "released", "@id": "/quality-metrics-fastqc/7964f8ac-4c6e-4146-ad9c-6d31fe36f6df/", "Total Sequences": 3052011, "uuid": "7964f8ac-4c6e-4146-ad9c-6d31fe36f6df", "display_title": "QualityMetricFastqc from 2024-12-05", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "overall_quality_status": "PASS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@type": ["FileFormat", "Item"], "display_title": "fastq", "status": "released", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "status": "current", "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"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Bing Ren, UCSD", "experiment_type": "single cell RNA-seq", "experiment_bucket": "raw file", "dataset": "scRNAseq in mouse eye tissue", "condition": "Donor 1 -  76 days old", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "retina", "lab_name": "Bing Ren, UCSD"}, "external_references": []}, {"uuid": "4207c47c-d6f9-4e59-a462-d8d0e8a80008", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "index reads (fastq)", "file_classification": "raw file", "status": "released", "upload_key": "4207c47c-d6f9-4e59-a462-d8d0e8a80008/4DNFIHXP7L5F.fastq.gz", "href": "/files-fastq/4DNFIHXP7L5F/@@download/4DNFIHXP7L5F.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/4207c47c-d6f9-4e59-a462-d8d0e8a80008/4DNFIHXP7L5F.fastq.gz", "accession": "4DNFIHXP7L5F", "md5sum": "7a80f58c0dbc64eeba2c56be15b7732a", "@id": "/files-fastq/4DNFIHXP7L5F/", "file_size": 27933675, "display_title": "4DNFIHXP7L5F.fastq.gz", "file_type": "index reads", "related_files": [{"relationship_type": "grouped with", "file": {"@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIYD6DB85/", "file_type_detailed": "reads (fastq)", "uuid": "1e4597a4-b0f0-475e-8a2a-409860ec700b", "display_title": "4DNFIYD6DB85.fastq.gz", "status": "released", "accession": "4DNFIYD6DB85", "paired_end": "1", "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"relationship_type": "grouped with", "file": {"@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFI21PLQYB/", "file_type_detailed": "reads (fastq)", "uuid": "53a8e48a-f878-4997-bffd-3dcffcecbaa3", "display_title": "4DNFI21PLQYB.fastq.gz", "status": "released", "accession": "4DNFI21PLQYB", "paired_end": "2", "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"Sequence length": "10", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIHXP7L5F/fastqc_report.html", "status": "released", "@id": "/quality-metrics-fastqc/ab8c5f23-463c-4c4f-8bbe-7cf28fbf76be/", "Total Sequences": 3052011, "uuid": "ab8c5f23-463c-4c4f-8bbe-7cf28fbf76be", "display_title": "QualityMetricFastqc from 2024-12-05", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "overall_quality_status": "PASS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@type": ["FileFormat", "Item"], "display_title": "fastq", "status": "released", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "status": "current", "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"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Bing Ren, UCSD", "experiment_type": "single cell RNA-seq", "experiment_bucket": "raw file", "dataset": "scRNAseq in mouse eye tissue", "condition": "Donor 1 -  76 days old", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "retina", "lab_name": "Bing Ren, UCSD"}, "external_references": []}, {"uuid": "1e4597a4-b0f0-475e-8a2a-409860ec700b", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "file_classification": "raw file", "paired_end": "1", "status": "released", "upload_key": "1e4597a4-b0f0-475e-8a2a-409860ec700b/4DNFIYD6DB85.fastq.gz", "href": "/files-fastq/4DNFIYD6DB85/@@download/4DNFIYD6DB85.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/1e4597a4-b0f0-475e-8a2a-409860ec700b/4DNFIYD6DB85.fastq.gz", "accession": "4DNFIYD6DB85", "md5sum": "157d34658d0b9cde937fb89ad2e5219a", "@id": "/files-fastq/4DNFIYD6DB85/", "file_size": 72598398, "display_title": "4DNFIYD6DB85.fastq.gz", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFI21PLQYB/", "file_type_detailed": "reads (fastq)", "uuid": "53a8e48a-f878-4997-bffd-3dcffcecbaa3", "display_title": "4DNFI21PLQYB.fastq.gz", "status": "released", "accession": "4DNFI21PLQYB", "paired_end": "2", "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"relationship_type": "grouped with", "file": {"@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIISKNNHN/", "file_type_detailed": "index reads (fastq)", "uuid": "7993b152-fbb6-4c7f-9d5c-797c6b14b4e3", "display_title": "4DNFIISKNNHN.fastq.gz", "status": "released", "accession": "4DNFIISKNNHN", "file_type": "index reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"relationship_type": "grouped with", "file": {"@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIHXP7L5F/", "file_type_detailed": "index reads (fastq)", "uuid": "4207c47c-d6f9-4e59-a462-d8d0e8a80008", "display_title": "4DNFIHXP7L5F.fastq.gz", "status": "released", "accession": "4DNFIHXP7L5F", "file_type": "index reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"Sequence length": "28", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIYD6DB85/fastqc_report.html", "status": "released", "@id": "/quality-metrics-fastqc/f81a0a9a-a969-4ff2-9d4f-7d6c51c28322/", "Total Sequences": 3052011, "uuid": "f81a0a9a-a969-4ff2-9d4f-7d6c51c28322", "display_title": "QualityMetricFastqc from 2024-12-05", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "overall_quality_status": "PASS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@type": ["FileFormat", "Item"], "display_title": "fastq", "status": "released", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "status": "current", "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"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Bing Ren, UCSD", "experiment_type": "single cell RNA-seq", "experiment_bucket": "raw file", "dataset": "scRNAseq in mouse eye tissue", "condition": "Donor 1 -  76 days old", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "retina", "lab_name": "Bing Ren, UCSD"}, "external_references": []}, {"uuid": "53a8e48a-f878-4997-bffd-3dcffcecbaa3", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "file_classification": "raw file", "paired_end": "2", "status": "released", "upload_key": "53a8e48a-f878-4997-bffd-3dcffcecbaa3/4DNFI21PLQYB.fastq.gz", "href": "/files-fastq/4DNFI21PLQYB/@@download/4DNFI21PLQYB.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/53a8e48a-f878-4997-bffd-3dcffcecbaa3/4DNFI21PLQYB.fastq.gz", "accession": "4DNFI21PLQYB", "md5sum": "a78d5a79eef90c2c174f0436b05a68da", "@id": "/files-fastq/4DNFI21PLQYB/", "file_size": 171446655, "display_title": "4DNFI21PLQYB.fastq.gz", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIYD6DB85/", "file_type_detailed": "reads (fastq)", "uuid": "1e4597a4-b0f0-475e-8a2a-409860ec700b", "display_title": "4DNFIYD6DB85.fastq.gz", "status": "released", "accession": "4DNFIYD6DB85", "paired_end": "1", "file_type": "reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"relationship_type": "grouped with", "file": {"@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIISKNNHN/", "file_type_detailed": "index reads (fastq)", "uuid": "7993b152-fbb6-4c7f-9d5c-797c6b14b4e3", "display_title": "4DNFIISKNNHN.fastq.gz", "status": "released", "accession": "4DNFIISKNNHN", "file_type": "index reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"relationship_type": "grouped with", "file": {"@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIHXP7L5F/", "file_type_detailed": "index reads (fastq)", "uuid": "4207c47c-d6f9-4e59-a462-d8d0e8a80008", "display_title": "4DNFIHXP7L5F.fastq.gz", "status": "released", "accession": "4DNFIHXP7L5F", "file_type": "index reads", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"Sequence length": "91", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI21PLQYB/fastqc_report.html", "status": "released", "@id": "/quality-metrics-fastqc/b84de26b-27d6-4166-91aa-4c007085be1b/", "Total Sequences": 3052011, "uuid": "b84de26b-27d6-4166-91aa-4c007085be1b", "display_title": "QualityMetricFastqc from 2024-12-05", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "overall_quality_status": "PASS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@type": ["FileFormat", "Item"], "display_title": "fastq", "status": "released", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"@type": ["Lab", "Item"], "status": "current", "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"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Bing Ren, UCSD", "experiment_type": "single cell RNA-seq", "experiment_bucket": "raw file", "dataset": "scRNAseq in mouse eye tissue", "condition": "Donor 1 -  76 days old", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "retina", "lab_name": "Bing Ren, UCSD"}, "external_references": []}], "biosample": {"biosample_type": "tissue", "uuid": "f4890506-849e-45bc-accc-8317da108bed", "status": "released", "biosource_summary": "retina", "@type": ["Biosample", "Item"], "treatments_summary": "None", "@id": "/biosamples/4DNBS1R9LE9N/", "modifications_summary": "None", "biosample_category": ["Multicellular Tissue"], "display_title": "4DNBS1R9LE9N", "accession": "4DNBS1R9LE9N", "biosource": [{"cell_line_tier": "Unclassified", "@id": "/biosources/4DNSROMTDV6E/", "display_title": "retina - 4DNSROMTDV6E", "uuid": "a539434c-a4ae-4ca5-aaa8-d00307db547b", "status": "released", "biosource_type": "tissue", "accession": "4DNSROMTDV6E", "@type": ["Biosource", "Item"], "tissue": {"display_title": "retina", "status": "released", "synonyms": ["tunica interna of eyeball", "inner layer of eyeball", "retina of camera-type eye"], "term_id": "UBERON:0000966", "uuid": "b428a669-bee5-4a2a-9729-5cdfb372571a", "@id": "/ontology-terms/UBERON:0000966/", "term_name": "retina", "@type": ["OntologyTerm", "Item"], "preferred_name": "retina", "slim_terms": [{"status": "released", "uuid": "111135bc-8535-4448-903e-854af460a233", "@id": "/ontology-terms/UBERON:0001032/", "display_title": "sensory system", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "uuid": "111119bc-8535-4448-903e-854af460a233", "@id": "/ontology-terms/UBERON:0000924/", "display_title": "ectoderm", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "uuid": "111181bc-8535-4448-903e-854af460a233", "@id": "/ontology-terms/UBERON:0000970/", "display_title": "eye", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "organism": {"@type": ["Organism", "Item"], "display_title": "M. musculus", "name": "mouse", "@id": "/organisms/10090/", "scientific_name": "Mus musculus", "status": "released", "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "tissue_organ_info": {"organ_system": ["sensory system", "ectoderm", "eye"], "tissue_source": "retina"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_type": {"title": "single cell RNA-seq", "@type": ["ExperimentType", "Item"], "assay_subclassification": "Transcription - Single Cell", "experiment_category": "Sequencing", "display_title": "single cell RNA-seq", "status": "released", "@id": "/experiment-types/single-cell-rna-seq/", "uuid": "b36947be-c260-4586-90b4-b321270ad706", "assay_classification": "RNA Quantification", "other_tags": ["1D", "Single Cell"], "assay_subclass_short": "Transcription", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_categorizer": {"field": "Default"}, "last_modified": {"date_modified": "2025-06-10T15:54:22.108282+00:00"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experimentset_type": "replicate", "other_processed_files": [{"type": "supplementary", "files": [{"@id": "/files-processed/4DNFIHEJ2CQQ/", "uuid": "442c0ca7-4700-4755-ba3c-ac341e482a77", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/442c0ca7-4700-4755-ba3c-ac341e482a77/4DNFIHEJ2CQQ.tsv.gz", "md5sum": "23712f06647b304cfaa17c5fb217e038", "file_size": 38275, "display_title": "4DNFIHEJ2CQQ.tsv.gz", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFIHEJ2CQQ", "file_type": "cell barcode", "status": "released", "file_type_detailed": "cell barcode (compressed_tsv)", "genome_assembly": "GRCm38", "file_format": {"status": "released", "display_title": "compressed_tsv", "@type": ["FileFormat", "Item"], "uuid": "c1b6d5b9-b98a-4350-ab77-b9b0b58da785", "@id": "/file-formats/compressed_tsv/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "href": "/files-processed/4DNFIHEJ2CQQ/@@download/4DNFIHEJ2CQQ.tsv.gz", "lab": {"@id": "/labs/bing-ren-lab/", "display_title": "Bing Ren, UCSD", "name": "bing-ren-lab", "@type": ["Lab", "Item"], "status": "current", "uuid": "795847de-20b6-4f8c-ba8d-185215469cbf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.795847de-20b6-4f8c-ba8d-185215469cbf"]}}, "track_and_facet_info": {"dataset": "scRNAseq in mouse eye tissue", "condition": "Donor 1 -  76 days old", "experimental_lab": "Bing Ren, UCSD", "replicate_info": "unreplicated", "experiment_bucket": "Processed files (contact matrix and filtered feature-barcode matrices)", "experiment_type": "single cell RNA-seq", "biosource_name": "retina", "lab_name": "Bing Ren, UCSD"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2025-06-16T17:51:55.170058+00:00"}}, {"@id": "/files-processed/4DNFIRO1NFED/", "uuid": "4ccc883f-dbf0-4bd1-b750-17a4cb8dc158", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/4ccc883f-dbf0-4bd1-b750-17a4cb8dc158/4DNFIRO1NFED.tsv.gz", "md5sum": "5c4b782a0859f46829a578007005e1ac", "file_size": 279361, "display_title": "4DNFIRO1NFED.tsv.gz", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFIRO1NFED", "file_type": "feature barcode", "status": "released", "file_type_detailed": "feature barcode (compressed_tsv)", "genome_assembly": "GRCm38", "file_format": {"status": "released", "display_title": "compressed_tsv", "@type": ["FileFormat", "Item"], "uuid": "c1b6d5b9-b98a-4350-ab77-b9b0b58da785", "@id": "/file-formats/compressed_tsv/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "href": "/files-processed/4DNFIRO1NFED/@@download/4DNFIRO1NFED.tsv.gz", "lab": {"@id": "/labs/bing-ren-lab/", "display_title": "Bing Ren, UCSD", "name": "bing-ren-lab", "@type": ["Lab", "Item"], "status": "current", "uuid": "795847de-20b6-4f8c-ba8d-185215469cbf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.795847de-20b6-4f8c-ba8d-185215469cbf"]}}, "track_and_facet_info": {"lab_name": "Bing Ren, UCSD"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2025-06-16T17:51:38.169940+00:00"}}, {"@id": "/files-processed/4DNFIOUMEQGB/", "uuid": "b93a1e27-5418-4b31-a86a-0ab748d0d5c1", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/b93a1e27-5418-4b31-a86a-0ab748d0d5c1/4DNFIOUMEQGB.matrix", "md5sum": "d9bb034ec28dab6c3cfc2db72e177c03", "file_size": 39082180, "display_title": "4DNFIOUMEQGB.matrix", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFIOUMEQGB", "file_type": "contact matrix", "status": "released", "file_type_detailed": "contact matrix (matrix)", "genome_assembly": "GRCm38", "file_format": {"status": "released", "display_title": "matrix", "@type": ["FileFormat", "Item"], "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce2", "@id": "/file-formats/matrix/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "href": "/files-processed/4DNFIOUMEQGB/@@download/4DNFIOUMEQGB.matrix", "lab": {"@id": "/labs/bing-ren-lab/", "display_title": "Bing Ren, UCSD", "name": "bing-ren-lab", "@type": ["Lab", "Item"], "status": "current", "uuid": "795847de-20b6-4f8c-ba8d-185215469cbf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.795847de-20b6-4f8c-ba8d-185215469cbf"]}}, "track_and_facet_info": {"dataset": "scRNAseq in mouse eye tissue", "condition": "Donor 1 -  76 days old", "experimental_lab": "Bing Ren, UCSD", "replicate_info": "unreplicated", "experiment_bucket": "Processed files (contact matrix and filtered feature-barcode matrices)", "experiment_type": "single cell RNA-seq", "biosource_name": "retina", "lab_name": "Bing Ren, UCSD"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2025-06-16T17:51:52.992755+00:00"}}], "title": "Processed files (contact matrix and filtered feature-barcode matrices)", "description": "Processed files for donor 1, retina tissue: 1) compressed .barcodes.tsv.gz and .features.tsv.gz file containing filtered feature-barcode matrices and 2) .matrix.mtx.gz containing contact matrix"}], "@id": "/experiment-set-replicates/4DNESN9LELPQ/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "3eaf1e6c-66ec-48db-a379-74bfb0258447", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNESN9LELPQ", "external_references": [], "pubs_using": [], "publications_of_set": [], "number_of_experiments": 1, "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/experiment-set-replicates/4DNESN9LELPQ/", "embedded_path": "badges", "item": {"messages": ["Replicate set contains only a single biological replicate"], "badge": {"commendation": null, "warning": "Replicate Numbers", "uuid": "24a64a84-3c33-4d76-aaf2-e5ef45eff347", "@id": "/badges/replicate-numbers/", "badge_icon": "/static/img/badges/replicates-orange-circle.svg", "description": "Issues with replicate numbers"}}}]}, "validation-errors": []}