{"lab": {"@type": ["Lab", "Item"], "correspondence": [{"contact_email": "cGV0ZXJfcGFya0BobXMuaGFydmFyZC5lZHU=", "@id": "/users/fb287a31-e765-41c5-8c1d-665f8e9f025b/", "display_title": "Peter Park"}], "status": "current", "display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "title": "4DN DCIC, HMS", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "award": {"@id": "/awards/1U01CA200059-01/", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "center_title": "DCIC - DCIC", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "description": "DCIC: The goals of the 4D Nucleome (4DN) Data Coordination and Integration Center (DCIC) are to collect, store, curate, display, and analyze data generated in the 4DN Network. We have assembled a team of investigators with a strong track record in analysis of chromatin interaction data, image processing and three-dimensional data visualization, integrative analysis of genomic and epigenomic data, data portal development, large-scale computing, and development of secure and flexible cloud technologies. In Aim 1, we will develop efficient submission pipelines for data and metadata from 4DN data production groups. We will define data/metadata requirements and quality metrics in conjunction with the production groups and ensure that high-quality, well- annotated data become available to the wider scientific community in a timely manner. In Aim 2, we will develop a user-friendly data portal for the broad scientific community. This portal will provide an easy-to-navigate interface for accessing raw and intermediate data files, allow for programmatic access via APIs, and will incorporate novel analysis and visualization tools developed by DCIC as well as other Network members. For computing and storage scalability and cost-effectiveness, significant efforts will be devoted to development and deployment of cloud-based technology. We will conduct tutorials and workshops to facilitate the use of 4DN data and tools by external investigators. In Aim 3, we will coordinate and assist in conducting integrative analysis of the multiple data types. These efforts will examine key questions in higher-order chromatin organization using both sequence and image data, and the tools and algorithms developed here will be incorporated into the data portal for use by other investigators. These three aims will ensure that the data generated in 4DN will have maximal impact for the scientific community.", "@type": ["Award", "Item"], "status": "current", "project": "4DN", "name": "1U01CA200059-01", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "b8475c1132e751ea7f5962ea738172f0", "status": "released", "accession": "4DNFI3W1178U", "file_size": 232607426, "file_type": "read positions", "description": "Positions of aligned reads in bed format, one line per read mate, for control experiment, from ENCODE ChIP-Seq Pipeline", "file_format": {"@id": "/file-formats/bed/", "@type": ["FileFormat", "Item"], "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "display_title": "bed", "status": "released", "file_format": "bed", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "date_created": "2020-08-28T20:59:51.956985+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2022-01-05T09:27:32.217589+00:00"}, "content_md5sum": "9c751c2b81cbe831a34ff65ca3321394", "public_release": "2020-09-08", "quality_metric": {"@type": ["QualityMetricChipseq", "QualityMetric", "Item"], "display_title": "QualityMetricChipseq from 2020-08-29", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI3W1178U/qc_report.html", "uuid": "942ac33d-0e47-4b32-8e93-755bafc8579f", "status": "released", "@id": "/quality-metrics-chipseq/942ac33d-0e47-4b32-8e93-755bafc8579f/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Nonredundant Read Fraction (NRF)", "value": "0.94", "tooltip": "distinct non-mito read pairs / total non-mito read pairs", "numberType": "float"}, {"title": "PCR Bottleneck Coefficient (PBC)", "value": "0.94", "tooltip": "one-read non-mito read pairs / distinct non-mito read pairs", "numberType": "float"}, {"title": "Filtered & Deduped Reads", "value": "13195345", "numberType": "integer"}]}, "schema_version": "3", "genome_assembly": "GRCm38", "project_release": "2020-09-08", "contributing_labs": [{"@id": "/labs/bing-ren-lab/", "status": "current", "uuid": "795847de-20b6-4f8c-ba8d-185215469cbf", "display_title": "Bing Ren, UCSD", "@type": ["Lab", "Item"], "correspondence": [{"contact_email": "YmlyZW5AdWNzZC5lZHU=", "@id": "/users/e3159ffc-a5a9-43a1-8cfa-90b776c39788/", "display_title": "Bing Ren"}], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.795847de-20b6-4f8c-ba8d-185215469cbf"]}}], "source_experiments": ["a4ed71d4-ee83-4151-abd6-df90ffed4a29"], "file_classification": "processed file", "@id": "/files-processed/4DNFI3W1178U/", "@type": ["FileProcessed", "File", "Item"], "uuid": "36798cba-08f8-40d4-adac-d6455d92b417", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNFI3W1178U.bed.gz", "external_references": [], "experiments": [{"display_title": "ChIP-seq against Rad21 mouse protein on F123-CASTx129 with Sox2 tags and RMCE site between Sox2 and its SE - 4DNEX5Y1P387", "uuid": "a4ed71d4-ee83-4151-abd6-df90ffed4a29", "accession": "4DNEX5Y1P387", "@type": ["ExperimentSeq", "Experiment", "Item"], "status": "released", "@id": "/experiments-seq/4DNEX5Y1P387/", "biosample": {"@id": "/biosamples/4DNBSLA64OHQ/", "display_title": "4DNBSLA64OHQ", "treatments_summary": "None", "accession": "4DNBSLA64OHQ", "@type": ["Biosample", "Item"], "biosource_summary": "F123-CASTx129 with Sox2 tags and RMCE site between Sox2 and its SE", "uuid": "da81c4b7-8843-445d-bdda-c597ad9d13bd", "modifications_summary": "RMCE replacement", "status": "released", "biosource": [{"display_title": "F123-CASTx129 with Sox2 tags and RMCE site between Sox2 and its SE - 4DNSR9TIV5EV", "uuid": "c1f610d2-a25d-400a-b807-5306c34fe3fc", "@id": "/biosources/4DNSR9TIV5EV/", "override_biosource_name": "F123-CASTx129 with Sox2 tags and RMCE site between Sox2 and its SE", "status": "released", "biosource_type": "stem cell derived cell line", "cell_line_tier": "Unclassified", "@type": ["Biosource", "Item"], "individual": {"@id": "/individuals-mouse/4DNINWEP34C1/", "uuid": "9eb64afa-705f-4710-a298-32ad67764d14", "display_title": "4DNINWEP34C1", "status": "released", "@type": ["IndividualMouse", "Individual", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/10090/", "name": "mouse", "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "status": "released", "@type": ["Organism", "Item"], "scientific_name": "Mus musculus", "display_title": "M. musculus", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "modifications": [{"display_title": "Crispr insertion for Sox2 mouse gene", "modification_type": "Crispr", "genomic_change": "insertion", "uuid": "8bf623f7-3894-4763-b286-4efed16c1755", "@type": ["Modification", "Item"], "status": "released", "@id": "/modifications/8bf623f7-3894-4763-b286-4efed16c1755/", "target_of_mod": [{"display_title": "Sox2 mouse gene", "@type": ["BioFeature", "Item"], "organism_name": "mouse", "uuid": "7b2a3877-409b-4575-b9e3-c92758d815c9", "@id": "/bio-features/7b2a3877-409b-4575-b9e3-c92758d815c9/", "status": "released", "feature_type": {"uuid": "0231da78-1adc-4b8a-89b9-4f91908412a3", "status": "released", "@id": "/ontology-terms/SO:0000704/", "display_title": "gene", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "relevant_genes": [{"uuid": "db4fa807-b3aa-4cf5-84da-3c0bb4d4c857", "status": "released", "@id": "/genes/20674/", "@type": ["Gene", "Item"], "display_title": "Sox2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "Crispr insertion for Sox2 mouse gene", "modification_type": "Crispr", "genomic_change": "insertion", "uuid": "cb04bb10-77a3-4123-bea1-985e97045cee", "@type": ["Modification", "Item"], "status": "released", "@id": "/modifications/cb04bb10-77a3-4123-bea1-985e97045cee/", "target_of_mod": [{"display_title": "Sox2 mouse gene", "@type": ["BioFeature", "Item"], "organism_name": "mouse", "uuid": "7b2a3877-409b-4575-b9e3-c92758d815c9", "@id": "/bio-features/7b2a3877-409b-4575-b9e3-c92758d815c9/", "status": "released", "feature_type": {"uuid": "0231da78-1adc-4b8a-89b9-4f91908412a3", "status": "released", "@id": "/ontology-terms/SO:0000704/", "display_title": "gene", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "relevant_genes": [{"uuid": "db4fa807-b3aa-4cf5-84da-3c0bb4d4c857", "status": "released", "@id": "/genes/20674/", "@type": ["Gene", "Item"], "display_title": "Sox2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "Crispr insertion", "modification_type": "Crispr", "genomic_change": "insertion", "uuid": "b201bb73-137d-4597-bb01-39f99019413c", "@type": ["Modification", "Item"], "status": "released", "@id": "/modifications/b201bb73-137d-4597-bb01-39f99019413c/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "tissue": {"uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "display_title": "stem cell", "preferred_name": "stem cell", "term_name": "stem cell", "term_id": "CL:0000034", "@id": "/ontology-terms/CL:0000034/", "@type": ["OntologyTerm", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "cell_line": {"@id": "/ontology-terms/EFO:0009319/", "uuid": "b75930ee-182a-4f7a-8360-ecd6b7ac532f", "@type": ["OntologyTerm", "Item"], "preferred_name": "F123-CASTx129", "status": "released", "term_name": "F123-CASTx129", "term_id": "EFO:0009319", "display_title": "F123-CASTx129", "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": [{"status": "released", "uuid": "61313987-1139-4d30-a957-537e7ce550bc", "display_title": "4DNESMQMWDI3", "@id": "/experiment-set-replicates/4DNESMQMWDI3/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "experimentset_type": "replicate", "accession": "4DNESMQMWDI3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "last_modified": {"date_modified": "2023-02-01T22:10:31.256839+00:00"}, "experiment_type": {"uuid": "47a593da-c458-422a-a974-82b3302e89cb", "@id": "/experiment-types/chip-seq/", "@type": ["ExperimentType", "Item"], "title": "ChIP-seq", "status": "released", "display_title": "ChIP-seq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "file_type_detailed": "read positions (bed)", "track_and_facet_info": {"experimental_lab": "Bing Ren, UCSD", "experiment_type": "ChIP-seq", "experiment_bucket": "processed file", "assay_info": "Rad21 mouse protein", "dataset": "ChIP-seq on tagged Sox2 cells", "condition": "15 syn non-boundary CTCF sites - anti-Rad21", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F123-CASTx129 with Sox2 tags and RMCE site between Sox2 and its SE", "lab_name": "4DN DCIC, HMS"}, "title": "4DNFI3W1178U", "href": "/files-processed/4DNFI3W1178U/@@download/4DNFI3W1178U.bed.gz", "upload_key": "36798cba-08f8-40d4-adac-d6455d92b417/4DNFI3W1178U.bed.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/36798cba-08f8-40d4-adac-d6455d92b417/4DNFI3W1178U.bed.gz", "tsv_notes": "", "workflow_run_inputs": [{"uuid": "7a7e7518-97a3-405e-9c7a-ef2059625bb0", "@id": "/workflow-runs-awsem/7a7e7518-97a3-405e-9c7a-ef2059625bb0/", "display_title": "encode-chipseq-postaln 1.1.1 run 2020-09-01 17:47:57.788019", "status": "released", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "output_files": [{"workflow_argument_name": "chip.optimal_peak", "value": {"@type": ["FileProcessed", "File", "Item"], "uuid": "bab9f4ec-6a65-4dc7-a506-2feafa2609cf", "display_title": "4DNFI43WTI7N.bb", "@id": "/files-processed/4DNFI43WTI7N/", "accession": "4DNFI43WTI7N", "status": "released", "file_format": {"@id": "/file-formats/bigbed/", "@type": ["FileFormat", "Item"], "display_title": "bigbed", "file_format": "bigbed", "uuid": "bbafb7f8-98d5-48d7-8e75-dc40a5186e19", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "chip.conservative_peak", "value": {"@type": ["FileProcessed", "File", "Item"], "uuid": "d4c78358-1e0f-4f42-aa4a-db81897bce29", "display_title": "4DNFIOZCZE1A.bb", "@id": "/files-processed/4DNFIOZCZE1A/", "accession": "4DNFIOZCZE1A", "status": "released", "file_format": {"@id": "/file-formats/bigbed/", "@type": ["FileFormat", "Item"], "display_title": "bigbed", "file_format": "bigbed", "uuid": "bbafb7f8-98d5-48d7-8e75-dc40a5186e19", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "chip.sig_fc", "value": {"@type": ["FileProcessed", "File", "Item"], "uuid": "ab39a6b2-f8ed-468f-b6d8-452bf939fac5", "display_title": "4DNFI36XIHUU.bw", "@id": "/files-processed/4DNFI36XIHUU/", "accession": "4DNFI36XIHUU", "status": "released", "file_format": {"@id": "/file-formats/bw/", "@type": ["FileFormat", "Item"], "display_title": "bw", "file_format": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "chip.report", "value_qc": {"overall_quality_status": "PASS", "@type": ["QualityMetricChipseq", "QualityMetric", "Item"], "status": "released", "uuid": "194403ae-2cdd-419d-8e7b-a18015cf9774", "display_title": "QualityMetricChipseq from 2020-09-01", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI43WTI7N/qc_report.html", "@id": "/quality-metrics-chipseq/194403ae-2cdd-419d-8e7b-a18015cf9774/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "chip.qc_json", "value_qc": {"overall_quality_status": "PASS", "@type": ["QualityMetricChipseq", "QualityMetric", "Item"], "status": "released", "uuid": "194403ae-2cdd-419d-8e7b-a18015cf9774", "display_title": "QualityMetricChipseq from 2020-09-01", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI43WTI7N/qc_report.html", "@id": "/quality-metrics-chipseq/194403ae-2cdd-419d-8e7b-a18015cf9774/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "input_files": [{"workflow_argument_name": "chip.blacklist", "value": {"@type": ["FileReference", "File", "Item"], "uuid": "a32747a3-8a9e-4a9e-a7a1-4db0e8b65925", "accession": "4DNFIZ3FBPK8", "@id": "/files-reference/4DNFIZ3FBPK8/", "status": "released", "filename": "mm10.blacklist.bed.gz", "display_title": "4DNFIZ3FBPK8.bed.gz", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/bed/", "status": "released", "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "display_title": "bed", "file_format": "bed", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "chip.chrsz", "value": {"@type": ["FileReference", "File", "Item"], "uuid": "be0a9819-d2ce-4422-be4b-234fb1677dd9", "accession": "4DNFIBP173GC", "@id": "/files-reference/4DNFIBP173GC/", "status": "released", "filename": "mm10_no_alt.chrom.sizes", "display_title": "4DNFIBP173GC.chrom.sizes", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/chromsizes/", "status": "released", "uuid": "d13d06cf-218e-4f61-55f0-93f226248b2c", "display_title": "chromsizes", "file_format": "chromsizes", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "chip.tas", "value": {"@type": ["FileProcessed", "File", "Item"], "uuid": "36798cba-08f8-40d4-adac-d6455d92b417", "accession": "4DNFI3W1178U", "@id": "/files-processed/4DNFI3W1178U/", "status": "released", "display_title": "4DNFI3W1178U.bed.gz", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/bed/", "status": "released", "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "display_title": "bed", "file_format": "bed", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "chip.tas", "value": {"@type": ["FileProcessed", "File", "Item"], "uuid": "eb092229-e4ea-4196-b458-35b7603985a0", "accession": "4DNFIKALWV9I", "@id": "/files-processed/4DNFIKALWV9I/", "status": "released", "display_title": "4DNFIKALWV9I.bed.gz", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/bed/", "status": "released", "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "display_title": "bed", "file_format": "bed", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "chip.bam2ta_no_filt_R1.ta", "value": {"@type": ["FileProcessed", "File", "Item"], "uuid": "de17e590-4c58-4e1c-8bb5-02e89c5b1613", "accession": "4DNFIPZ1N6GU", "@id": "/files-processed/4DNFIPZ1N6GU/", "status": "released", "display_title": "4DNFIPZ1N6GU.bed.gz", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/bed/", "status": "released", "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "display_title": "bed", "file_format": "bed", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "chip.bam2ta_no_filt_R1.ta", "value": {"@type": ["FileProcessed", "File", "Item"], "uuid": "2c0abeda-6fe9-47d8-b407-3f6232bca749", "accession": "4DNFIW3GI5BN", "@id": "/files-processed/4DNFIW3GI5BN/", "status": "released", "display_title": "4DNFIW3GI5BN.bed.gz", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/bed/", "status": "released", "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "display_title": "bed", "file_format": "bed", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "chip.ctl_tas", "value": {"@type": ["FileProcessed", "File", "Item"], "uuid": "8de920fb-ff53-4508-94ee-b31858fd941f", "accession": "4DNFI2387Q44", "@id": "/files-processed/4DNFI2387Q44/", "status": "released", "display_title": "4DNFI2387Q44.bed.gz", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/bed/", "status": "released", "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "display_title": "bed", "file_format": "bed", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "chip.ctl_tas", "value": {"@type": ["FileProcessed", "File", "Item"], "uuid": "8482ed28-8f80-4a0f-a55d-eae4608efa92", "accession": "4DNFI28SATLZ", "@id": "/files-processed/4DNFI28SATLZ/", "status": "released", "display_title": "4DNFI28SATLZ.bed.gz", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/bed/", "status": "released", "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "display_title": "bed", "file_format": "bed", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"title": "Chip-seq data processing pipeline, post-alignment 1.1.1", "display_title": "Chip-seq data processing pipeline, post-alignment 1.1.1 - 4DNWF3BT781I", "uuid": "1f04547b-7d26-43a4-888d-2d8a4595f513", "@id": "/workflows/4DNWF3BT781I/", "status": "released", "@type": ["Workflow", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"error": "no view permissions"}], "workflow_run_outputs": [{"status": "released", "display_title": "encode-chipseq-aln-chip 1.1.1 run 2020-08-28 20:59:57.292738", "@id": "/workflow-runs-awsem/7e88654b-f6a3-4bd2-8bc3-d0f7d46cee05/", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "uuid": "7e88654b-f6a3-4bd2-8bc3-d0f7d46cee05", "output_files": [{"workflow_argument_name": "chip.first_ta", "value": {"@type": ["FileProcessed", "File", "Item"], "uuid": "36798cba-08f8-40d4-adac-d6455d92b417", "display_title": "4DNFI3W1178U.bed.gz", "status": "released", "accession": "4DNFI3W1178U", "@id": "/files-processed/4DNFI3W1178U/", "file_format": {"uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "@id": "/file-formats/bed/", "@type": ["FileFormat", "Item"], "file_format": "bed", "display_title": "bed", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "chip.first_ta_xcor", "value": {"@type": ["FileProcessed", "File", "Item"], "uuid": "de17e590-4c58-4e1c-8bb5-02e89c5b1613", "display_title": "4DNFIPZ1N6GU.bed.gz", "status": "released", "accession": "4DNFIPZ1N6GU", "@id": "/files-processed/4DNFIPZ1N6GU/", "file_format": {"uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "@id": "/file-formats/bed/", "@type": ["FileFormat", "Item"], "file_format": "bed", "display_title": "bed", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "chip.report", "value_qc": {"@type": ["QualityMetricChipseq", "QualityMetric", "Item"], "uuid": "942ac33d-0e47-4b32-8e93-755bafc8579f", "overall_quality_status": "PASS", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI3W1178U/qc_report.html", "@id": "/quality-metrics-chipseq/942ac33d-0e47-4b32-8e93-755bafc8579f/", "display_title": "QualityMetricChipseq from 2020-08-29", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "chip.qc_json", "value_qc": {"@type": ["QualityMetricChipseq", "QualityMetric", "Item"], "uuid": "942ac33d-0e47-4b32-8e93-755bafc8579f", "overall_quality_status": "PASS", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI3W1178U/qc_report.html", "@id": "/quality-metrics-chipseq/942ac33d-0e47-4b32-8e93-755bafc8579f/", "display_title": "QualityMetricChipseq from 2020-08-29", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "input_files": [{"workflow_argument_name": "chip.bwa_idx_tar", "value": {"status": "released", "display_title": "4DNFIZ2PWCC2.bwaIndex.tar", "uuid": "f4b63d31-65d8-437f-a76a-6bedbb52ae6f", "@id": "/files-reference/4DNFIZ2PWCC2/", "accession": "4DNFIZ2PWCC2", "filename": "mm10.bwaIndex.tar", "@type": ["FileReference", "File", "Item"], "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "file_format": "uncompressed_bwaIndex", "@id": "/file-formats/uncompressed_bwaIndex/", "uuid": "96809e57-4ccd-40b4-9fcb-ce27c4f16df9", "display_title": "uncompressed_bwaIndex", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "chip.blacklist", "value": {"status": "released", "display_title": "4DNFIZ3FBPK8.bed.gz", "uuid": "a32747a3-8a9e-4a9e-a7a1-4db0e8b65925", "@id": "/files-reference/4DNFIZ3FBPK8/", "accession": "4DNFIZ3FBPK8", "filename": "mm10.blacklist.bed.gz", "@type": ["FileReference", "File", "Item"], "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "file_format": "bed", "@id": "/file-formats/bed/", "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "display_title": "bed", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "chip.chrsz", "value": {"status": "released", "display_title": "4DNFIBP173GC.chrom.sizes", "uuid": "be0a9819-d2ce-4422-be4b-234fb1677dd9", "@id": "/files-reference/4DNFIBP173GC/", "accession": "4DNFIBP173GC", "filename": "mm10_no_alt.chrom.sizes", "@type": ["FileReference", "File", "Item"], "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "file_format": "chromsizes", "@id": "/file-formats/chromsizes/", "uuid": "d13d06cf-218e-4f61-55f0-93f226248b2c", "display_title": "chromsizes", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "chip.fastqs", "value": {"status": "released", "display_title": "4DNFIPKPFPC4.fastq.gz", "uuid": "7f703f9d-238b-4186-9fca-3fc31cb919d4", "@id": "/files-fastq/4DNFIPKPFPC4/", "accession": "4DNFIPKPFPC4", "filename": "HH752_R1.fastq.gz", "@type": ["FileFastq", "File", "Item"], "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "file_format": "fastq", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "chip.fastqs", "value": {"status": "released", "display_title": "4DNFI3RH7827.fastq.gz", "uuid": "94d141c4-9fb0-45c1-b974-13662a4a571a", "@id": "/files-fastq/4DNFI3RH7827/", "accession": "4DNFI3RH7827", "filename": "HH752_R2.fastq.gz", "@type": ["FileFastq", "File", "Item"], "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "file_format": "fastq", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"@id": "/workflows/4DNWF25VHY99/", "display_title": "Chip-seq data processing pipeline, Align-only, ChIP 1.1.1 - 4DNWF25VHY99", "title": "Chip-seq data processing pipeline, Align-only, ChIP 1.1.1", "@type": ["Workflow", "Item"], "uuid": "1dfb78e8-9844-48c6-804e-d05e7257e178", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_sets": [], "source_experiment_sets": [{"display_title": "4DNESMQMWDI3", "status": "released", "uuid": "61313987-1139-4d30-a957-537e7ce550bc", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "@id": "/experiment-set-replicates/4DNESMQMWDI3/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@context": "/terms/", "aggregated-items": {"last_modified": [{"parent": "/experiments-seq/4DNEX5Y1P387/", "embedded_path": "experiments.last_modified", "item": {"date_modified": "2023-02-01T22:10:31.256839+00:00"}}, {"parent": "/files-processed/4DNFI3W1178U/", "embedded_path": "last_modified", "item": {"date_modified": "2022-01-05T09:27:32.217589+00:00"}}]}, "validation-errors": []}