{"lab": {"display_title": "Giacomo Cavalli, UM", "uuid": "c38cf2e8-1129-48e1-b8a4-d42e88258e30", "@id": "/labs/giacomo-cavalli-lab/", "status": "current", "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", "project": "External", "@type": ["Award", "Item"], "center_title": "External", "display_title": "EXTERNAL AWARD", "@id": "/awards/external-award/", "center": "External", "status": "current", "name": "external-award", "description": "Funding source is from outside 4DN.", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "7304b08fa48212b0bc87056135efccf9", "status": "released", "aliases": ["4dn-dcic-lab:SRR5863575_1_fq"], "dbxrefs": ["SRA:SRR5863575"], "filename": "SRR5863575_1.fastq.gz", "accession": "4DNFITJZM7WX", "file_size": 9829109937, "file_type": "reads", "instrument": "Illumina HiSeq 2000", "paired_end": "1", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "file_format": "fastq", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "read_length": 49, "date_created": "2019-08-12T14:54:51.661669+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2020-04-06T23:45:04.437525+00:00"}, "related_files": [{"file": {"uuid": "ef0bec77-18c4-4ac2-bade-18e3f65295de", "display_title": "4DNFIUHWC2WP.fastq.gz", "@id": "/files-fastq/4DNFIUHWC2WP/", "accession": "4DNFIUHWC2WP", "status": "released", "@type": ["FileFastq", "File", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "relationship_type": "paired with"}], "content_md5sum": "7db092adbd51a321ef30f0106ff15a26", "public_release": "2019-12-01", "quality_metric": {"display_title": "QualityMetricFastqc from 2019-08-21", "overall_quality_status": "PASS", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFITJZM7WX/fastqc_report.html", "Sequence length": "49", "@id": "/quality-metrics-fastqc/ca5b5a66-eea5-489e-b4f7-6eaaa4ff60ef/", "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 322219363, "uuid": "ca5b5a66-eea5-489e-b4f7-6eaaa4ff60ef", "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/4DNFITJZM7WX/", "@type": ["FileFastq", "File", "Item"], "uuid": "c0fe8d54-3dbc-4ae2-bdd3-caf119885f05", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNFITJZM7WX.fastq.gz", "external_references": [{"ref": "SRA:SRR5863575", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5863575"}], "experiments": [{"display_title": "in situ Hi-C on ES-E14TG2a with DpnII - 4DNEXYBNSCM1", "status": "released", "@type": ["ExperimentHiC", "Experiment", "Item"], "@id": "/experiments-hi-c/4DNEXYBNSCM1/", "uuid": "edee8435-e585-44b1-bf2b-9c2deb1ba89d", "accession": "4DNEXYBNSCM1", "biosample": {"@type": ["Biosample", "Item"], "uuid": "49edf9d2-db4c-472f-a7c9-92c8125450b3", "status": "released", "accession": "4DNBSG83E3O3", "biosource_summary": "ES-E14TG2a", "@id": "/biosamples/4DNBSG83E3O3/", "treatments_summary": "None", "display_title": "4DNBSG83E3O3", "modifications_summary": "Stable Transfection insertion and Crispr insertion for Zfp608 mouse gene", "biosource": [{"@id": "/biosources/4DNSRQDR15QF/", "cell_line_tier": "Unclassified", "status": "released", "display_title": "ES-E14TG2a - 4DNSRQDR15QF", "@type": ["Biosource", "Item"], "uuid": "09df211d-62d9-439a-b546-81a8a6f463bc", "biosource_type": "stem cell derived cell line", "tissue": {"term_name": "stem cell", "term_id": "CL:0000034", "status": "released", "@id": "/ontology-terms/CL:0000034/", "preferred_name": "stem cell", "display_title": "stem cell", "@type": ["OntologyTerm", "Item"], "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"display_title": "4DNINOXRXEQP", "@type": ["IndividualMouse", "Individual", "Item"], "@id": "/individuals-mouse/4DNINOXRXEQP/", "uuid": "1b2fa35a-6173-431f-b2e2-db2e18017870", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "cell_line": {"preferred_name": "ES-E14TG2a", "@type": ["OntologyTerm", "Item"], "term_name": "ES-E14TG2a", "display_title": "ES-E14TG2a", "uuid": "2262fd9b-3185-4c65-8ad5-bfe65e986954", "term_id": "EFO:0006275", "@id": "/ontology-terms/EFO:0006275/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"status": "released", "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "@id": "/organisms/10090/", "display_title": "M. musculus", "name": "mouse", "scientific_name": "Mus musculus", "@type": ["Organism", "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"]}}, "experiment_type": {"uuid": "a2920a38-cdba-4ff0-b4f0-c6bb53257747", "display_title": "in situ Hi-C", "title": "in situ Hi-C", "status": "released", "@id": "/experiment-types/in-situ-hi-c/", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_sets": [{"uuid": "eb1f0c7a-9cba-43fb-bfa9-52316a38be8f", "experimentset_type": "replicate", "@id": "/experiment-set-replicates/4DNESGC3Z7E3/", "display_title": "4DNESGC3Z7E3", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "status": "released", "accession": "4DNESGC3Z7E3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "digestion_enzyme": {"display_title": "DpnII", "@id": "/enzymes/DpnII/", "@type": ["Enzyme", "Item"], "status": "released", "uuid": "356a57a1-1f1d-463d-a972-27742f79a6a5", "name": "DpnII", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2024-08-01T21:08:54.016337+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "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 - zfp608 gRNA with empty dCas9", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "ES-E14TG2a", "lab_name": "Giacomo Cavalli, UM"}, "title": "4DNFITJZM7WX", "href": "/files-fastq/4DNFITJZM7WX/@@download/4DNFITJZM7WX.fastq.gz", "upload_key": "c0fe8d54-3dbc-4ae2-bdd3-caf119885f05/4DNFITJZM7WX.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/c0fe8d54-3dbc-4ae2-bdd3-caf119885f05/4DNFITJZM7WX.fastq.gz", "tsv_notes": "", "workflow_run_inputs": [{"uuid": "5e3d2ff5-7e6f-4785-9d7a-ffbe88a7b3dc", "@id": "/workflow-runs-awsem/5e3d2ff5-7e6f-4785-9d7a-ffbe88a7b3dc/", "display_title": "md5 0.2.6 run 2019-08-21 13:32:16.728039", "status": "released", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "input_files": [{"workflow_argument_name": "input_file", "value": {"status": "released", "filename": "SRR5863575_1.fastq.gz", "display_title": "4DNFITJZM7WX.fastq.gz", "uuid": "c0fe8d54-3dbc-4ae2-bdd3-caf119885f05", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFITJZM7WX/", "accession": "4DNFITJZM7WX", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "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", "uuid": "c77a117b-9a58-477e-aaa5-291a109a99f6", "status": "released", "display_title": "md5 0.2.6 - 4DNWF2HFF82B", "@id": "/workflows/4DNWF2HFF82B/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "output_files": [{"workflow_argument_name": "report"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "271501db-9de3-4603-86df-bf951ddcfa92", "@id": "/workflow-runs-awsem/271501db-9de3-4603-86df-bf951ddcfa92/", "display_title": "fastqc v1 run 2019-08-21 23:13:14.802715", "status": "released", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "input_files": [{"workflow_argument_name": "input_fastq", "value": {"status": "released", "filename": "SRR5863575_1.fastq.gz", "display_title": "4DNFITJZM7WX.fastq.gz", "uuid": "c0fe8d54-3dbc-4ae2-bdd3-caf119885f05", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFITJZM7WX/", "accession": "4DNFITJZM7WX", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"@type": ["Workflow", "Item"], "title": "FastQC v1", "uuid": "2324ad76-ff37-4157-8bcc-3ce72b7dace9", "status": "released", "display_title": "FastQC v1 - 4DNWFAW5VTA5", "@id": "/workflows/4DNWFAW5VTA5/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "output_files": [{"workflow_argument_name": "report_zip", "value_qc": {"uuid": "ca5b5a66-eea5-489e-b4f7-6eaaa4ff60ef", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "overall_quality_status": "PASS", "status": "released", "@id": "/quality-metrics-fastqc/ca5b5a66-eea5-489e-b4f7-6eaaa4ff60ef/", "display_title": "QualityMetricFastqc from 2019-08-21", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFITJZM7WX/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "4da93652-8660-498d-bec9-d1603529fcdc", "@id": "/workflow-runs-awsem/4da93652-8660-498d-bec9-d1603529fcdc/", "display_title": "bwa-mem 0.2.6 run 2019-10-16 01:02:49.636449", "status": "released", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "input_files": [{"workflow_argument_name": "bwa_index", "value": {"status": "released", "filename": "mm10.bwaIndex.tgz", "display_title": "4DNFI823LSI8.bwaIndex.tgz", "uuid": "4a6d10ee-2edb-4402-a98f-0edb1d58f5e1", "@type": ["FileReference", "File", "Item"], "@id": "/files-reference/4DNFI823LSI8/", "accession": "4DNFI823LSI8", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bwaIndex", "uuid": "d13d06cf-218e-4f61-55f0-91f226248b2c", "file_format": "bwaIndex", "status": "released", "@id": "/file-formats/bwaIndex/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "fastq1", "value": {"status": "released", "filename": "SRR5863575_1.fastq.gz", "display_title": "4DNFITJZM7WX.fastq.gz", "uuid": "c0fe8d54-3dbc-4ae2-bdd3-caf119885f05", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFITJZM7WX/", "accession": "4DNFITJZM7WX", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "fastq2", "value": {"status": "released", "filename": "SRR5863575_2.fastq.gz", "display_title": "4DNFIUHWC2WP.fastq.gz", "uuid": "ef0bec77-18c4-4ac2-bade-18e3f65295de", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIUHWC2WP/", "accession": "4DNFIUHWC2WP", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "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", "uuid": "3feedadc-50f9-4bb4-919b-09a8b731d0cc", "status": "released", "display_title": "Alignment for Hi-C using bwa-mem 0.2.6 - 4DNWF84NFOQP", "@id": "/workflows/4DNWF84NFOQP/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "output_files": [{"workflow_argument_name": "out_bam", "value": {"display_title": "4DNFI35G2F5N.bam", "@type": ["FileProcessed", "File", "Item"], "status": "released", "uuid": "f63de3b1-01f9-4444-996d-e74037251ddb", "accession": "4DNFI35G2F5N", "@id": "/files-processed/4DNFI35G2F5N/", "file_format": {"@id": "/file-formats/bam/", "display_title": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "file_format": "bam", "@type": ["FileFormat", "Item"], "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"]}}, {"uuid": "f20b01eb-2ca3-4fb8-bbd9-c5ec95315fdc", "@id": "/workflow-runs-awsem/f20b01eb-2ca3-4fb8-bbd9-c5ec95315fdc/", "display_title": "fastq-first-line v2 run 2020-04-06 23:39:53.580332", "status": "released", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "input_files": [{"workflow_argument_name": "fastq", "value": {"status": "released", "filename": "SRR5863575_1.fastq.gz", "display_title": "4DNFITJZM7WX.fastq.gz", "uuid": "c0fe8d54-3dbc-4ae2-bdd3-caf119885f05", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFITJZM7WX/", "accession": "4DNFITJZM7WX", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "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", "uuid": "93a1a931-d55d-4623-adfb-0fa735daf6ae", "status": "released", "display_title": "Getting first line of fastq file - 4DNWFASTQFO1", "@id": "/workflows/4DNWFASTQFO1/", "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": []}