{"lab": {"uuid": "c38cf2e8-1129-48e1-b8a4-d42e88258e30", "@id": "/labs/giacomo-cavalli-lab/", "status": "current", "title": "Giacomo Cavalli, UM", "display_title": "Giacomo Cavalli, UM", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.c38cf2e8-1129-48e1-b8a4-d42e88258e30"]}}, "award": {"uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "@id": "/awards/external-award/", "center": "External", "@type": ["Award", "Item"], "display_title": "EXTERNAL AWARD", "name": "external-award", "description": "Funding source is from outside 4DN.", "center_title": "External", "project": "External", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "5068762bb351b9409d844c5887f78552", "status": "released", "aliases": ["4dn-dcic-lab:SRR5863583_2_fq"], "dbxrefs": ["SRA:SRR5863583"], "filename": "SRR5863583_2.fastq.gz", "accession": "4DNFIIKOJEX3", "file_size": 11219919077, "file_type": "reads", "instrument": "Illumina HiSeq 2000", "paired_end": "2", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "status": "released", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "read_length": 49, "date_created": "2019-08-12T14:55:06.482464+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2020-04-06T23:43:02.700743+00:00"}, "related_files": [{"file": {"status": "released", "@id": "/files-fastq/4DNFIDVY621I/", "accession": "4DNFIDVY621I", "display_title": "4DNFIDVY621I.fastq.gz", "@type": ["FileFastq", "File", "Item"], "uuid": "b520737f-f1bb-41ee-8cad-d68907322bdd", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "relationship_type": "paired with"}], "content_md5sum": "792d9c7aed5225f8cee96f540d8bb5e7", "public_release": "2019-12-01", "quality_metric": {"Total Sequences": 338101307, "display_title": "QualityMetricFastqc from 2019-08-21", "Sequence length": "49", "@id": "/quality-metrics-fastqc/3159c28e-d93b-4fb6-8c11-38515d8f593a/", "overall_quality_status": "PASS", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIIKOJEX3/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "3159c28e-d93b-4fb6-8c11-38515d8f593a", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "schema_version": "2", "file_first_line": "@1", "project_release": "2019-12-01", "file_classification": "raw file", "@id": "/files-fastq/4DNFIIKOJEX3/", "@type": ["FileFastq", "File", "Item"], "uuid": "60ad3da3-ffb2-435e-bb71-7205e52e78c5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNFIIKOJEX3.fastq.gz", "external_references": [{"ref": "SRA:SRR5863583", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5863583"}], "experiments": [{"status": "released", "@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "d2507bb9-5fcb-42a6-83bd-d0b6093b7617", "display_title": "in situ Hi-C on ES-E14TG2a with DpnII - 4DNEX5O7D76E", "accession": "4DNEX5O7D76E", "@id": "/experiments-hi-c/4DNEX5O7D76E/", "biosample": {"@type": ["Biosample", "Item"], "status": "released", "@id": "/biosamples/4DNBSQV58OA8/", "modifications_summary": "Stable Transfection insertion and Crispr insertion for Sox4 mouse gene", "accession": "4DNBSQV58OA8", "treatments_summary": "None", "uuid": "a937a09c-b35a-4d97-8f18-63ae8ec265e0", "biosource_summary": "ES-E14TG2a", "display_title": "4DNBSQV58OA8", "biosource": [{"@id": "/biosources/4DNSRQDR15QF/", "uuid": "09df211d-62d9-439a-b546-81a8a6f463bc", "status": "released", "biosource_type": "stem cell derived cell line", "@type": ["Biosource", "Item"], "display_title": "ES-E14TG2a - 4DNSRQDR15QF", "cell_line_tier": "Unclassified", "tissue": {"display_title": "stem cell", "@id": "/ontology-terms/CL:0000034/", "preferred_name": "stem cell", "status": "released", "term_name": "stem cell", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "@type": ["OntologyTerm", "Item"], "term_id": "CL:0000034", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "organism": {"@type": ["Organism", "Item"], "name": "mouse", "display_title": "M. musculus", "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "status": "released", "@id": "/organisms/10090/", "scientific_name": "Mus musculus", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"status": "released", "@type": ["IndividualMouse", "Individual", "Item"], "uuid": "1b2fa35a-6173-431f-b2e2-db2e18017870", "@id": "/individuals-mouse/4DNINOXRXEQP/", "display_title": "4DNINOXRXEQP", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "cell_line": {"term_name": "ES-E14TG2a", "display_title": "ES-E14TG2a", "term_id": "EFO:0006275", "status": "released", "@id": "/ontology-terms/EFO:0006275/", "uuid": "2262fd9b-3185-4c65-8ad5-bfe65e986954", "@type": ["OntologyTerm", "Item"], "preferred_name": "ES-E14TG2a", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_type": {"@id": "/experiment-types/in-situ-hi-c/", "display_title": "in situ Hi-C", "status": "released", "title": "in situ Hi-C", "uuid": "a2920a38-cdba-4ff0-b4f0-c6bb53257747", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_sets": [{"experimentset_type": "replicate", "display_title": "4DNES68MSHVU", "accession": "4DNES68MSHVU", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "5176fdd5-804e-484e-b275-b0f0426a977f", "status": "released", "@id": "/experiment-set-replicates/4DNES68MSHVU/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "digestion_enzyme": {"@id": "/enzymes/DpnII/", "display_title": "DpnII", "@type": ["Enzyme", "Item"], "uuid": "356a57a1-1f1d-463d-a972-27742f79a6a5", "name": "DpnII", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2024-08-01T21:08:56.335933+00:00"}}], "file_type_detailed": "reads (fastq)", "track_and_facet_info": {"experimental_lab": "Giacomo Cavalli, UM", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "dataset": "Hi-C on E14Tg2 cell line", "condition": "control - sox4 gRNA with empty dCas9", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "ES-E14TG2a", "lab_name": "Giacomo Cavalli, UM"}, "title": "4DNFIIKOJEX3", "href": "/files-fastq/4DNFIIKOJEX3/@@download/4DNFIIKOJEX3.fastq.gz", "upload_key": "60ad3da3-ffb2-435e-bb71-7205e52e78c5/4DNFIIKOJEX3.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/60ad3da3-ffb2-435e-bb71-7205e52e78c5/4DNFIIKOJEX3.fastq.gz", "tsv_notes": "", "workflow_run_inputs": [{"@id": "/workflow-runs-awsem/9344fcbc-e7c7-41d4-8a4b-7aed8c2f2e8c/", "status": "released", "display_title": "md5 0.2.6 run 2019-08-21 13:31:54.650287", "uuid": "9344fcbc-e7c7-41d4-8a4b-7aed8c2f2e8c", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "input_files": [{"workflow_argument_name": "input_file", "value": {"status": "released", "accession": "4DNFIIKOJEX3", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIIKOJEX3/", "display_title": "4DNFIIKOJEX3.fastq.gz", "filename": "SRR5863583_2.fastq.gz", "uuid": "60ad3da3-ffb2-435e-bb71-7205e52e78c5", "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"@type": ["Workflow", "Item"], "title": "md5 0.2.6", "status": "released", "@id": "/workflows/4DNWF2HFF82B/", "display_title": "md5 0.2.6 - 4DNWF2HFF82B", "uuid": "c77a117b-9a58-477e-aaa5-291a109a99f6", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "output_files": [{"workflow_argument_name": "report"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/workflow-runs-awsem/a1364785-2aaf-4e44-9fce-c1fdb5aba40b/", "status": "released", "display_title": "fastqc v1 run 2019-08-21 23:12:45.893976", "uuid": "a1364785-2aaf-4e44-9fce-c1fdb5aba40b", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "input_files": [{"workflow_argument_name": "input_fastq", "value": {"status": "released", "accession": "4DNFIIKOJEX3", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIIKOJEX3/", "display_title": "4DNFIIKOJEX3.fastq.gz", "filename": "SRR5863583_2.fastq.gz", "uuid": "60ad3da3-ffb2-435e-bb71-7205e52e78c5", "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"@type": ["Workflow", "Item"], "title": "FastQC v1", "status": "released", "@id": "/workflows/4DNWFAW5VTA5/", "display_title": "FastQC v1 - 4DNWFAW5VTA5", "uuid": "2324ad76-ff37-4157-8bcc-3ce72b7dace9", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "output_files": [{"workflow_argument_name": "report_zip", "value_qc": {"uuid": "3159c28e-d93b-4fb6-8c11-38515d8f593a", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIIKOJEX3/fastqc_report.html", "status": "released", "@id": "/quality-metrics-fastqc/3159c28e-d93b-4fb6-8c11-38515d8f593a/", "display_title": "QualityMetricFastqc from 2019-08-21", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "overall_quality_status": "PASS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/workflow-runs-awsem/28edddc7-ab42-496e-9ddf-bc11447358ff/", "status": "released", "display_title": "bwa-mem 0.2.6 run 2019-10-16 01:02:59.895502", "uuid": "28edddc7-ab42-496e-9ddf-bc11447358ff", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "input_files": [{"workflow_argument_name": "bwa_index", "value": {"status": "released", "accession": "4DNFI823LSI8", "@type": ["FileReference", "File", "Item"], "@id": "/files-reference/4DNFI823LSI8/", "display_title": "4DNFI823LSI8.bwaIndex.tgz", "filename": "mm10.bwaIndex.tgz", "uuid": "4a6d10ee-2edb-4402-a98f-0edb1d58f5e1", "file_format": {"@id": "/file-formats/bwaIndex/", "file_format": "bwaIndex", "status": "released", "@type": ["FileFormat", "Item"], "display_title": "bwaIndex", "uuid": "d13d06cf-218e-4f61-55f0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "fastq1", "value": {"status": "released", "accession": "4DNFIDVY621I", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIDVY621I/", "display_title": "4DNFIDVY621I.fastq.gz", "filename": "SRR5863583_1.fastq.gz", "uuid": "b520737f-f1bb-41ee-8cad-d68907322bdd", "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "fastq2", "value": {"status": "released", "accession": "4DNFIIKOJEX3", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIIKOJEX3/", "display_title": "4DNFIIKOJEX3.fastq.gz", "filename": "SRR5863583_2.fastq.gz", "uuid": "60ad3da3-ffb2-435e-bb71-7205e52e78c5", "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"@type": ["Workflow", "Item"], "title": "Alignment for Hi-C using bwa-mem 0.2.6", "status": "released", "@id": "/workflows/4DNWF84NFOQP/", "display_title": "Alignment for Hi-C using bwa-mem 0.2.6 - 4DNWF84NFOQP", "uuid": "3feedadc-50f9-4bb4-919b-09a8b731d0cc", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "output_files": [{"workflow_argument_name": "out_bam", "value": {"uuid": "ebfe3514-bc3e-4bf9-a0a4-6d45f278ffe4", "display_title": "4DNFINO9S2MP.bam", "accession": "4DNFINO9S2MP", "@id": "/files-processed/4DNFINO9S2MP/", "@type": ["FileProcessed", "File", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "bam", "file_format": "bam", "@id": "/file-formats/bam/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/workflow-runs-awsem/1ef04f8a-5f7e-4480-8c36-23704791ae60/", "status": "released", "display_title": "fastq-first-line v2 run 2020-04-06 23:37:51.999021", "uuid": "1ef04f8a-5f7e-4480-8c36-23704791ae60", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "input_files": [{"workflow_argument_name": "fastq", "value": {"status": "released", "accession": "4DNFIIKOJEX3", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIIKOJEX3/", "display_title": "4DNFIIKOJEX3.fastq.gz", "filename": "SRR5863583_2.fastq.gz", "uuid": "60ad3da3-ffb2-435e-bb71-7205e52e78c5", "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"@type": ["Workflow", "Item"], "title": "Getting first line of fastq file", "status": "released", "@id": "/workflows/4DNWFASTQFO1/", "display_title": "Getting first line of fastq file - 4DNWFASTQFO1", "uuid": "93a1a931-d55d-4623-adfb-0fa735daf6ae", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "output_files": [{"workflow_argument_name": "first_line"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "workflow_run_outputs": [], "@context": "/terms/", "aggregated-items": {}, "validation-errors": []}