{"lab": {"uuid": "cf5abe29-1cf9-4413-b02e-664b47a6d53d", "title": "Ana Pombo, MDC", "@id": "/labs/ana-pombo-lab/", "@type": ["Lab", "Item"], "display_title": "Ana Pombo, MDC", "status": "current", "correspondence": [{"contact_email": "YW5hLnBvbWJvQG1kYy1iZXJsaW4uZGU=", "@id": "/users/bce4f2b5-9a2a-4db2-9dd6-7d61f19025c1/", "display_title": "Ana Pombo"}], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.cf5abe29-1cf9-4413-b02e-664b47a6d53d"]}}, "award": {"project": "4DN", "display_title": "CENTER FOR INTEGRATED MULTI-MODAL AND MULTI-SCALE NUCLEOME RESEARCH", "uuid": "ee89349a-1d43-4048-9142-bc750f0f3b32", "center_title": "CDIMV - Ren", "name": "1UM1HG011585-01", "@type": ["Award", "Item"], "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.", "@id": "/awards/1UM1HG011585-01/", "status": "current", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "7ca54378de456572a289a6780fd3e797", "status": "released", "aliases": ["ana-pombo-lab:experiment_gam_VTACocRepl1_GAM180117_0NP_H06_1_S48_R1_001.fastq.gz"], "filename": "VTACocRepl1_GAM180117_0NP_H06_1_S48_R1_001.fastq.gz", "accession": "4DNFIJKY7GHX", "file_size": 185779719, "file_type": "reads", "instrument": "NextSeq500/550", "file_format": {"@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "display_title": "fastq", "status": "released", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "read_length": 75, "date_created": "2024-02-09T19:28:12.039472+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2024-06-26T16:54:49.466345+00:00"}, "content_md5sum": "1dea59eb1089dd17c7a9597998bab253", "public_release": "2024-05-23", "quality_metric": {"@id": "/quality-metrics-fastqc/7f656223-f4c7-4f12-91e9-632861a2c9af/", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "7f656223-f4c7-4f12-91e9-632861a2c9af", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIJKY7GHX/fastqc_report.html", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2024-02-12", "Sequence length": "35-75", "status": "released", "Total Sequences": 3741372, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "schema_version": "2", "file_first_line": "@NB501326:156:H3MK3BGX5:1:11101:25501:1062 1:N:0:TAGGCATG+CGGAGATA", "project_release": "2024-05-08", "file_classification": "raw file", "@id": "/files-fastq/4DNFIJKY7GHX/", "@type": ["FileFastq", "File", "Item"], "uuid": "4a8e57a8-1c43-4fd6-8376-9101f8e904c0", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNFIJKY7GHX.fastq.gz", "external_references": [], "experiments": [{"status": "released", "uuid": "f4953b8f-d6b6-408e-ae13-0cf02d4ffee0", "accession": "4DNEXFT12BYV", "@id": "/experiments-seq/4DNEXFT12BYV/", "display_title": "GAM on ventral tegmental area - 4DNEXFT12BYV", "@type": ["ExperimentSeq", "Experiment", "Item"], "biosample": {"display_title": "4DNBSOFKQWWJ", "@id": "/biosamples/4DNBSOFKQWWJ/", "modifications_summary": "None", "treatments_summary": "cocaine treatment (15.0 mg/kg body weight)", "biosource_summary": "ventral tegmental area", "uuid": "300e3c00-981f-43c4-9797-de4371878498", "@type": ["Biosample", "Item"], "status": "released", "accession": "4DNBSOFKQWWJ", "biosource": [{"uuid": "db3d2eaf-9b2c-4af7-96eb-b24ea0e58101", "@type": ["Biosource", "Item"], "status": "released", "@id": "/biosources/4DNSRRFK44DB/", "cell_line_tier": "Unclassified", "biosource_type": "tissue", "display_title": "ventral tegmental area - 4DNSRRFK44DB", "tissue": {"uuid": "9c5b3fd2-b6ee-4817-8fa2-145c76999719", "preferred_name": "ventral tegmental area", "@type": ["OntologyTerm", "Item"], "term_id": "UBERON:0002691", "status": "released", "term_name": "ventral tegmental area", "display_title": "ventral tegmental area", "@id": "/ontology-terms/UBERON:0002691/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/10090/", "name": "mouse", "display_title": "M. musculus", "@type": ["Organism", "Item"], "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "status": "released", "scientific_name": "Mus musculus", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"@id": "/individuals-mouse/4DNIN6LCB27S/", "display_title": "4DNIN6LCB27S", "@type": ["IndividualMouse", "Individual", "Item"], "uuid": "a3985a45-6373-4809-908f-21bc6547ca3e", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_sets": [{"@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "@id": "/experiment-set-replicates/4DNESMAQEPWU/", "uuid": "70acc460-44c5-4407-b92f-3385cf87c39a", "accession": "4DNESMAQEPWU", "display_title": "4DNESMAQEPWU", "experimentset_type": "replicate", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_type": {"title": "GAM", "uuid": "1c41d7cc-8bfb-402f-b752-9db223de86f4", "@type": ["ExperimentType", "Item"], "display_title": "GAM", "status": "released", "@id": "/experiment-types/gam/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2024-05-23T00:10:11.718811+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "file_type_detailed": "reads (fastq)", "track_and_facet_info": {"experimental_lab": "Ana Pombo, MDC", "experiment_type": "GAM", "experiment_bucket": "raw file", "dataset": "GAM on mouse dopaminergic VTA neurons post cocaine", "condition": "TH-GFP strain - 24 hours post cocaine treatment", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "ventral tegmental area", "lab_name": "Ana Pombo, MDC"}, "title": "4DNFIJKY7GHX", "href": "/files-fastq/4DNFIJKY7GHX/@@download/4DNFIJKY7GHX.fastq.gz", "upload_key": "4a8e57a8-1c43-4fd6-8376-9101f8e904c0/4DNFIJKY7GHX.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/4a8e57a8-1c43-4fd6-8376-9101f8e904c0/4DNFIJKY7GHX.fastq.gz", "tsv_notes": "", "workflow_run_inputs": [{"status": "released", "uuid": "e5653109-b302-4a14-9e66-eaa85b6af0ad", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "@id": "/workflow-runs-awsem/e5653109-b302-4a14-9e66-eaa85b6af0ad/", "display_title": "md5 0.2.6 run 2024-02-12 03:33:09.495905", "output_files": [{"workflow_argument_name": "report"}], "input_files": [{"workflow_argument_name": "input_file", "value": {"accession": "4DNFIJKY7GHX", "@id": "/files-fastq/4DNFIJKY7GHX/", "@type": ["FileFastq", "File", "Item"], "status": "released", "uuid": "4a8e57a8-1c43-4fd6-8376-9101f8e904c0", "filename": "VTACocRepl1_GAM180117_0NP_H06_1_S48_R1_001.fastq.gz", "display_title": "4DNFIJKY7GHX.fastq.gz", "file_format": {"file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "display_title": "fastq", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"@id": "/workflows/4DNWF2HFF82B/", "uuid": "c77a117b-9a58-477e-aaa5-291a109a99f6", "title": "md5 0.2.6", "display_title": "md5 0.2.6 - 4DNWF2HFF82B", "status": "released", "@type": ["Workflow", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "uuid": "6f7c2c98-1bc3-4412-82c1-51e84745d0b0", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "@id": "/workflow-runs-awsem/6f7c2c98-1bc3-4412-82c1-51e84745d0b0/", "display_title": "fastqc v2 run 2024-02-12 23:07:24.156545", "output_files": [{"workflow_argument_name": "report_zip", "value_qc": {"@id": "/quality-metrics-fastqc/7f656223-f4c7-4f12-91e9-632861a2c9af/", "uuid": "7f656223-f4c7-4f12-91e9-632861a2c9af", "display_title": "QualityMetricFastqc from 2024-02-12", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIJKY7GHX/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "overall_quality_status": "PASS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "input_files": [{"workflow_argument_name": "input_fastq", "value": {"accession": "4DNFIJKY7GHX", "@id": "/files-fastq/4DNFIJKY7GHX/", "@type": ["FileFastq", "File", "Item"], "status": "released", "uuid": "4a8e57a8-1c43-4fd6-8376-9101f8e904c0", "filename": "VTACocRepl1_GAM180117_0NP_H06_1_S48_R1_001.fastq.gz", "display_title": "4DNFIJKY7GHX.fastq.gz", "file_format": {"file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "display_title": "fastq", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"@id": "/workflows/4DNWFAEU2GB7/", "uuid": "49e96b51-ed6c-4418-a693-d0e9f79adfa5", "title": "FastQC v2", "display_title": "FastQC v2 - 4DNWFAEU2GB7", "status": "released", "@type": ["Workflow", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "uuid": "530a4959-fdba-43c2-bb8e-f632f5dd534d", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "@id": "/workflow-runs-awsem/530a4959-fdba-43c2-bb8e-f632f5dd534d/", "display_title": "fastq-first-line v2 run 2024-02-13 04:48:01.121900", "output_files": [{"workflow_argument_name": "first_line"}], "input_files": [{"workflow_argument_name": "fastq", "value": {"accession": "4DNFIJKY7GHX", "@id": "/files-fastq/4DNFIJKY7GHX/", "@type": ["FileFastq", "File", "Item"], "status": "released", "uuid": "4a8e57a8-1c43-4fd6-8376-9101f8e904c0", "filename": "VTACocRepl1_GAM180117_0NP_H06_1_S48_R1_001.fastq.gz", "display_title": "4DNFIJKY7GHX.fastq.gz", "file_format": {"file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "display_title": "fastq", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"@id": "/workflows/4DNWFASTQFO1/", "uuid": "93a1a931-d55d-4623-adfb-0fa735daf6ae", "title": "Getting first line of fastq file", "display_title": "Getting first line of fastq file - 4DNWFASTQFO1", "status": "released", "@type": ["Workflow", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "workflow_run_outputs": [], "@context": "/terms/", "aggregated-items": {}, "validation-errors": []}