{"lab": {"status": "current", "@type": ["Lab", "Item"], "title": "Giacomo Cavalli, UM", "@id": "/labs/giacomo-cavalli-lab/", "uuid": "c38cf2e8-1129-48e1-b8a4-d42e88258e30", "display_title": "Giacomo Cavalli, UM", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.c38cf2e8-1129-48e1-b8a4-d42e88258e30"]}}, "award": {"@id": "/awards/external-award/", "center": "External", "uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "description": "Funding source is from outside 4DN.", "name": "external-award", "center_title": "External", "project": "External", "display_title": "EXTERNAL AWARD", "@type": ["Award", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "463a757f24571165b813ccbf11e27078", "status": "released", "aliases": ["4dn-dcic-lab:SRR5863570_1_fq"], "dbxrefs": ["SRA:SRR5863570"], "filename": "SRR5863570_1.fastq.gz", "accession": "4DNFI2ZT68WZ", "file_size": 9654101674, "file_type": "reads", "instrument": "Illumina HiSeq 2000", "paired_end": "1", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "read_length": 49, "date_created": "2019-08-12T14:54:40.006769+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2020-04-06T23:46:14.963468+00:00"}, "related_files": [{"file": {"accession": "4DNFIJAQAVJQ", "display_title": "4DNFIJAQAVJQ.fastq.gz", "@id": "/files-fastq/4DNFIJAQAVJQ/", "uuid": "236ad343-2197-49dc-ba15-18775ce99c99", "@type": ["FileFastq", "File", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "relationship_type": "paired with"}], "content_md5sum": "99f400d8ebee418f3294c245c3b35b7f", "public_release": "2019-12-01", "quality_metric": {"@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "overall_quality_status": "PASS", "Total Sequences": 314752632, "display_title": "QualityMetricFastqc from 2019-08-20", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI2ZT68WZ/fastqc_report.html", "status": "released", "uuid": "afa17911-fad1-4e0c-a3e0-b19771112067", "@id": "/quality-metrics-fastqc/afa17911-fad1-4e0c-a3e0-b19771112067/", "Sequence length": "49", "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/4DNFI2ZT68WZ/", "@type": ["FileFastq", "File", "Item"], "uuid": "6bc4095c-4615-4754-95f6-d367175a96ce", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNFI2ZT68WZ.fastq.gz", "external_references": [{"ref": "SRA:SRR5863570", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5863570"}], "experiments": [{"status": "released", "display_title": "in situ Hi-C on ES-E14TG2a with DpnII - 4DNEXGGI1YTN", "accession": "4DNEXGGI1YTN", "uuid": "4c530b75-73c2-419d-8a98-5513f68eadb5", "@id": "/experiments-hi-c/4DNEXGGI1YTN/", "@type": ["ExperimentHiC", "Experiment", "Item"], "biosample": {"accession": "4DNBSZRRI5YZ", "modifications_summary": "Crispr insertion for Zfp608 mouse gene", "treatments_summary": "None", "display_title": "4DNBSZRRI5YZ", "uuid": "f182e7ec-5a60-4061-ba5d-ce9c05240b33", "@type": ["Biosample", "Item"], "@id": "/biosamples/4DNBSZRRI5YZ/", "biosource_summary": "ES-E14TG2a", "status": "released", "biosource": [{"@type": ["Biosource", "Item"], "status": "released", "display_title": "ES-E14TG2a - 4DNSRQDR15QF", "@id": "/biosources/4DNSRQDR15QF/", "uuid": "09df211d-62d9-439a-b546-81a8a6f463bc", "biosource_type": "stem cell derived cell line", "cell_line_tier": "Unclassified", "cell_line": {"@id": "/ontology-terms/EFO:0006275/", "term_id": "EFO:0006275", "term_name": "ES-E14TG2a", "@type": ["OntologyTerm", "Item"], "display_title": "ES-E14TG2a", "uuid": "2262fd9b-3185-4c65-8ad5-bfe65e986954", "preferred_name": "ES-E14TG2a", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@type": ["Organism", "Item"], "scientific_name": "Mus musculus", "@id": "/organisms/10090/", "display_title": "M. musculus", "name": "mouse", "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"term_name": "stem cell", "display_title": "stem cell", "status": "released", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/CL:0000034/", "term_id": "CL:0000034", "preferred_name": "stem cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"@id": "/individuals-mouse/4DNINOXRXEQP/", "@type": ["IndividualMouse", "Individual", "Item"], "uuid": "1b2fa35a-6173-431f-b2e2-db2e18017870", "status": "released", "display_title": "4DNINOXRXEQP", "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": {"status": "released", "uuid": "a2920a38-cdba-4ff0-b4f0-c6bb53257747", "display_title": "in situ Hi-C", "@type": ["ExperimentType", "Item"], "@id": "/experiment-types/in-situ-hi-c/", "title": "in situ Hi-C", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "digestion_enzyme": {"status": "released", "display_title": "DpnII", "@type": ["Enzyme", "Item"], "@id": "/enzymes/DpnII/", "uuid": "356a57a1-1f1d-463d-a972-27742f79a6a5", "name": "DpnII", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_sets": [{"@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "experimentset_type": "replicate", "status": "released", "@id": "/experiment-set-replicates/4DNESXS1M9JR/", "display_title": "4DNESXS1M9JR", "accession": "4DNESXS1M9JR", "uuid": "532d75d8-e4a9-4258-83b2-bb86ac04f62d", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "last_modified": {"date_modified": "2024-08-01T21:08:57.985376+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 - zfp608 gRNA without dCas9", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "ES-E14TG2a", "lab_name": "Giacomo Cavalli, UM"}, "title": "4DNFI2ZT68WZ", "href": "/files-fastq/4DNFI2ZT68WZ/@@download/4DNFI2ZT68WZ.fastq.gz", "upload_key": "6bc4095c-4615-4754-95f6-d367175a96ce/4DNFI2ZT68WZ.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/6bc4095c-4615-4754-95f6-d367175a96ce/4DNFI2ZT68WZ.fastq.gz", "tsv_notes": "", "workflow_run_inputs": [{"display_title": "md5 0.2.6 run 2019-08-20 21:33:32.586968", "@id": "/workflow-runs-awsem/838fc9a0-9750-4510-b55f-4803a5b921ae/", "uuid": "838fc9a0-9750-4510-b55f-4803a5b921ae", "status": "released", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "output_files": [{"workflow_argument_name": "report"}], "input_files": [{"workflow_argument_name": "input_file", "value": {"status": "released", "@id": "/files-fastq/4DNFI2ZT68WZ/", "uuid": "6bc4095c-4615-4754-95f6-d367175a96ce", "filename": "SRR5863570_1.fastq.gz", "accession": "4DNFI2ZT68WZ", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFI2ZT68WZ.fastq.gz", "file_format": {"@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "status": "released", "file_format": "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"], "@id": "/workflows/4DNWF2HFF82B/", "uuid": "c77a117b-9a58-477e-aaa5-291a109a99f6", "status": "released", "title": "md5 0.2.6", "display_title": "md5 0.2.6 - 4DNWF2HFF82B", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "fastqc v1 run 2019-08-20 21:33:34.692435", "@id": "/workflow-runs-awsem/54fccb31-90f3-4351-8d48-50916eabf2c2/", "uuid": "54fccb31-90f3-4351-8d48-50916eabf2c2", "status": "released", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "output_files": [{"workflow_argument_name": "report_zip", "value_qc": {"@id": "/quality-metrics-fastqc/afa17911-fad1-4e0c-a3e0-b19771112067/", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI2ZT68WZ/fastqc_report.html", "uuid": "afa17911-fad1-4e0c-a3e0-b19771112067", "display_title": "QualityMetricFastqc from 2019-08-20", "overall_quality_status": "PASS", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "input_files": [{"workflow_argument_name": "input_fastq", "value": {"status": "released", "@id": "/files-fastq/4DNFI2ZT68WZ/", "uuid": "6bc4095c-4615-4754-95f6-d367175a96ce", "filename": "SRR5863570_1.fastq.gz", "accession": "4DNFI2ZT68WZ", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFI2ZT68WZ.fastq.gz", "file_format": {"@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "status": "released", "file_format": "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"], "@id": "/workflows/4DNWFAW5VTA5/", "uuid": "2324ad76-ff37-4157-8bcc-3ce72b7dace9", "status": "released", "title": "FastQC v1", "display_title": "FastQC v1 - 4DNWFAW5VTA5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "bwa-mem 0.2.6 run 2019-10-16 01:03:04.994433", "@id": "/workflow-runs-awsem/11db88cd-808a-4e36-9f8f-6f59a30e0fe9/", "uuid": "11db88cd-808a-4e36-9f8f-6f59a30e0fe9", "status": "released", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "output_files": [{"workflow_argument_name": "out_bam", "value": {"accession": "4DNFI2IV6R94", "uuid": "7a3d0f0f-144e-453a-84b1-59fcda706d21", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFI2IV6R94.bam", "status": "released", "@id": "/files-processed/4DNFI2IV6R94/", "file_format": {"status": "released", "display_title": "bam", "file_format": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "input_files": [{"workflow_argument_name": "bwa_index", "value": {"status": "released", "@id": "/files-reference/4DNFI823LSI8/", "uuid": "4a6d10ee-2edb-4402-a98f-0edb1d58f5e1", "filename": "mm10.bwaIndex.tgz", "accession": "4DNFI823LSI8", "@type": ["FileReference", "File", "Item"], "display_title": "4DNFI823LSI8.bwaIndex.tgz", "file_format": {"@id": "/file-formats/bwaIndex/", "@type": ["FileFormat", "Item"], "display_title": "bwaIndex", "status": "released", "file_format": "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", "@id": "/files-fastq/4DNFI2ZT68WZ/", "uuid": "6bc4095c-4615-4754-95f6-d367175a96ce", "filename": "SRR5863570_1.fastq.gz", "accession": "4DNFI2ZT68WZ", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFI2ZT68WZ.fastq.gz", "file_format": {"@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "status": "released", "file_format": "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", "@id": "/files-fastq/4DNFIJAQAVJQ/", "uuid": "236ad343-2197-49dc-ba15-18775ce99c99", "filename": "SRR5863570_2.fastq.gz", "accession": "4DNFIJAQAVJQ", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIJAQAVJQ.fastq.gz", "file_format": {"@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "status": "released", "file_format": "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"], "@id": "/workflows/4DNWF84NFOQP/", "uuid": "3feedadc-50f9-4bb4-919b-09a8b731d0cc", "status": "released", "title": "Alignment for Hi-C using bwa-mem 0.2.6", "display_title": "Alignment for Hi-C using bwa-mem 0.2.6 - 4DNWF84NFOQP", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "fastq-first-line v2 run 2020-04-06 23:41:03.915114", "@id": "/workflow-runs-awsem/f2ce05ce-8192-494d-87e9-81864c3c6dd3/", "uuid": "f2ce05ce-8192-494d-87e9-81864c3c6dd3", "status": "released", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "output_files": [{"workflow_argument_name": "first_line"}], "input_files": [{"workflow_argument_name": "fastq", "value": {"status": "released", "@id": "/files-fastq/4DNFI2ZT68WZ/", "uuid": "6bc4095c-4615-4754-95f6-d367175a96ce", "filename": "SRR5863570_1.fastq.gz", "accession": "4DNFI2ZT68WZ", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFI2ZT68WZ.fastq.gz", "file_format": {"@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "status": "released", "file_format": "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"], "@id": "/workflows/4DNWFASTQFO1/", "uuid": "93a1a931-d55d-4623-adfb-0fa735daf6ae", "status": "released", "title": "Getting first line of fastq file", "display_title": "Getting first line of fastq file - 4DNWFASTQFO1", "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": []}