{"lab": {"title": "Giacomo Cavalli, UM", "display_title": "Giacomo Cavalli, UM", "@id": "/labs/giacomo-cavalli-lab/", "status": "current", "uuid": "c38cf2e8-1129-48e1-b8a4-d42e88258e30", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.c38cf2e8-1129-48e1-b8a4-d42e88258e30"]}}, "award": {"status": "current", "@id": "/awards/external-award/", "uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "display_title": "EXTERNAL AWARD", "@type": ["Award", "Item"], "center_title": "External", "description": "Funding source is from outside 4DN.", "name": "external-award", "project": "External", "center": "External", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "f6def07610b975027cd30a52e89c77cd", "status": "released", "aliases": ["4dn-dcic-lab:SRR5863572_1_fq"], "dbxrefs": ["SRA:SRR5863572"], "filename": "SRR5863572_1.fastq.gz", "accession": "4DNFINMOVEEF", "file_size": 9993196503, "file_type": "reads", "instrument": "Illumina HiSeq 2000", "paired_end": "1", "file_format": {"@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "display_title": "fastq", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "read_length": 49, "date_created": "2019-08-12T14:54:45.619121+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2020-04-06T23:45:46.501260+00:00"}, "related_files": [{"file": {"@type": ["FileFastq", "File", "Item"], "display_title": "4DNFI5QPSCYN.fastq.gz", "@id": "/files-fastq/4DNFI5QPSCYN/", "uuid": "81404c74-bdbc-47bc-9170-fd790fb0d0a1", "status": "released", "accession": "4DNFI5QPSCYN", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "relationship_type": "paired with"}], "content_md5sum": "915057dc5f6119600907dc15fae6d42d", "public_release": "2019-12-01", "quality_metric": {"Sequence length": "49", "@id": "/quality-metrics-fastqc/f3abe99a-4fdd-4916-9dbd-ac2f06e8083f/", "uuid": "f3abe99a-4fdd-4916-9dbd-ac2f06e8083f", "overall_quality_status": "PASS", "status": "released", "display_title": "QualityMetricFastqc from 2019-08-21", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFINMOVEEF/fastqc_report.html", "Total Sequences": 326824340, "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/4DNFINMOVEEF/", "@type": ["FileFastq", "File", "Item"], "uuid": "168dd42b-b5d7-402b-b977-cc513c8c6e1d", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNFINMOVEEF.fastq.gz", "external_references": [{"ref": "SRA:SRR5863572", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5863572"}], "experiments": [{"@id": "/experiments-hi-c/4DNEXTJ6TT4G/", "status": "released", "display_title": "in situ Hi-C on ES-E14TG2a with DpnII - 4DNEXTJ6TT4G", "uuid": "bad3e79c-9108-4d4c-8e7d-62ade4db0bfd", "accession": "4DNEXTJ6TT4G", "@type": ["ExperimentHiC", "Experiment", "Item"], "biosample": {"biosource_summary": "ES-E14TG2a", "modifications_summary": "Stable Transfection insertion and Crispr insertion for Zfp608 mouse gene", "treatments_summary": "None", "@type": ["Biosample", "Item"], "status": "released", "@id": "/biosamples/4DNBSGOM7RU7/", "uuid": "3127e6f5-97d0-4cf9-9746-e4a674ed1ba0", "display_title": "4DNBSGOM7RU7", "accession": "4DNBSGOM7RU7", "biosource": [{"cell_line_tier": "Unclassified", "biosource_type": "stem cell derived cell line", "display_title": "ES-E14TG2a - 4DNSRQDR15QF", "@type": ["Biosource", "Item"], "status": "released", "@id": "/biosources/4DNSRQDR15QF/", "uuid": "09df211d-62d9-439a-b546-81a8a6f463bc", "organism": {"name": "mouse", "status": "released", "display_title": "M. musculus", "@id": "/organisms/10090/", "@type": ["Organism", "Item"], "scientific_name": "Mus musculus", "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/CL:0000034/", "status": "released", "term_name": "stem cell", "display_title": "stem cell", "term_id": "CL:0000034", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "preferred_name": "stem cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"status": "released", "@id": "/individuals-mouse/4DNINOXRXEQP/", "display_title": "4DNINOXRXEQP", "uuid": "1b2fa35a-6173-431f-b2e2-db2e18017870", "@type": ["IndividualMouse", "Individual", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "cell_line": {"status": "released", "preferred_name": "ES-E14TG2a", "uuid": "2262fd9b-3185-4c65-8ad5-bfe65e986954", "term_name": "ES-E14TG2a", "@id": "/ontology-terms/EFO:0006275/", "term_id": "EFO:0006275", "@type": ["OntologyTerm", "Item"], "display_title": "ES-E14TG2a", "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", "@type": ["ExperimentType", "Item"], "title": "in situ Hi-C", "@id": "/experiment-types/in-situ-hi-c/", "display_title": "in situ Hi-C", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_sets": [{"@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "@id": "/experiment-set-replicates/4DNES3Y26CEU/", "status": "released", "uuid": "1dcf6aa4-c30a-4ee7-b956-68616682c4c2", "experimentset_type": "replicate", "display_title": "4DNES3Y26CEU", "accession": "4DNES3Y26CEU", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "digestion_enzyme": {"@id": "/enzymes/DpnII/", "uuid": "356a57a1-1f1d-463d-a972-27742f79a6a5", "status": "released", "display_title": "DpnII", "name": "DpnII", "@type": ["Enzyme", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2024-08-01T21:08:48.583419+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": "zfp608 activation with dCas9-VP64", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "ES-E14TG2a", "lab_name": "Giacomo Cavalli, UM"}, "title": "4DNFINMOVEEF", "href": "/files-fastq/4DNFINMOVEEF/@@download/4DNFINMOVEEF.fastq.gz", "upload_key": "168dd42b-b5d7-402b-b977-cc513c8c6e1d/4DNFINMOVEEF.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/168dd42b-b5d7-402b-b977-cc513c8c6e1d/4DNFINMOVEEF.fastq.gz", "tsv_notes": "", "workflow_run_inputs": [{"display_title": "fastqc v1 run 2019-08-21 13:36:12.945949", "uuid": "99280c1a-439e-49f5-95b4-107957da9057", "@id": "/workflow-runs-awsem/99280c1a-439e-49f5-95b4-107957da9057/", "status": "released", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "output_files": [{"workflow_argument_name": "report_zip", "value_qc": {"@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "f3abe99a-4fdd-4916-9dbd-ac2f06e8083f", "display_title": "QualityMetricFastqc from 2019-08-21", "@id": "/quality-metrics-fastqc/f3abe99a-4fdd-4916-9dbd-ac2f06e8083f/", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFINMOVEEF/fastqc_report.html", "overall_quality_status": "PASS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "input_files": [{"workflow_argument_name": "input_fastq", "value": {"filename": "SRR5863572_1.fastq.gz", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFINMOVEEF", "display_title": "4DNFINMOVEEF.fastq.gz", "uuid": "168dd42b-b5d7-402b-b977-cc513c8c6e1d", "@id": "/files-fastq/4DNFINMOVEEF/", "status": "released", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "display_title": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"status": "released", "@type": ["Workflow", "Item"], "display_title": "FastQC v1 - 4DNWFAW5VTA5", "title": "FastQC v1", "uuid": "2324ad76-ff37-4157-8bcc-3ce72b7dace9", "@id": "/workflows/4DNWFAW5VTA5/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "md5 0.2.6 run 2019-08-20 21:17:25.344420", "uuid": "d87d60b2-43ce-4ae9-8424-eac0387e6b97", "@id": "/workflow-runs-awsem/d87d60b2-43ce-4ae9-8424-eac0387e6b97/", "status": "released", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "output_files": [{"workflow_argument_name": "report"}], "input_files": [{"workflow_argument_name": "input_file", "value": {"filename": "SRR5863572_1.fastq.gz", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFINMOVEEF", "display_title": "4DNFINMOVEEF.fastq.gz", "uuid": "168dd42b-b5d7-402b-b977-cc513c8c6e1d", "@id": "/files-fastq/4DNFINMOVEEF/", "status": "released", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "display_title": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"status": "released", "@type": ["Workflow", "Item"], "display_title": "md5 0.2.6 - 4DNWF2HFF82B", "title": "md5 0.2.6", "uuid": "c77a117b-9a58-477e-aaa5-291a109a99f6", "@id": "/workflows/4DNWF2HFF82B/", "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 01:02:24.157781", "uuid": "2482a59f-b7dc-48c6-b771-942057c05a4e", "@id": "/workflow-runs-awsem/2482a59f-b7dc-48c6-b771-942057c05a4e/", "status": "released", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "output_files": [{"workflow_argument_name": "out_bam", "value": {"status": "released", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFIEMVJS34", "uuid": "0dad32c9-2c91-4dd9-b6a7-db29bae1b12a", "@id": "/files-processed/4DNFIEMVJS34/", "display_title": "4DNFIEMVJS34.bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bam", "file_format": "bam", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@id": "/file-formats/bam/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "input_files": [{"workflow_argument_name": "bwa_index", "value": {"filename": "mm10.bwaIndex.tgz", "@type": ["FileReference", "File", "Item"], "accession": "4DNFI823LSI8", "display_title": "4DNFI823LSI8.bwaIndex.tgz", "uuid": "4a6d10ee-2edb-4402-a98f-0edb1d58f5e1", "@id": "/files-reference/4DNFI823LSI8/", "status": "released", "file_format": {"uuid": "d13d06cf-218e-4f61-55f0-91f226248b2c", "@id": "/file-formats/bwaIndex/", "display_title": "bwaIndex", "status": "released", "@type": ["FileFormat", "Item"], "file_format": "bwaIndex", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "fastq1", "value": {"filename": "SRR5863572_1.fastq.gz", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFINMOVEEF", "display_title": "4DNFINMOVEEF.fastq.gz", "uuid": "168dd42b-b5d7-402b-b977-cc513c8c6e1d", "@id": "/files-fastq/4DNFINMOVEEF/", "status": "released", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "display_title": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "fastq2", "value": {"filename": "SRR5863572_2.fastq.gz", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFI5QPSCYN", "display_title": "4DNFI5QPSCYN.fastq.gz", "uuid": "81404c74-bdbc-47bc-9170-fd790fb0d0a1", "@id": "/files-fastq/4DNFI5QPSCYN/", "status": "released", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "display_title": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"status": "released", "@type": ["Workflow", "Item"], "display_title": "Alignment for Hi-C using bwa-mem 0.2.6 - 4DNWF84NFOQP", "title": "Alignment for Hi-C using bwa-mem 0.2.6", "uuid": "3feedadc-50f9-4bb4-919b-09a8b731d0cc", "@id": "/workflows/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 23:40:35.787685", "uuid": "75c5eda0-545c-469c-a7cf-46516979708e", "@id": "/workflow-runs-awsem/75c5eda0-545c-469c-a7cf-46516979708e/", "status": "released", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "output_files": [{"workflow_argument_name": "first_line"}], "input_files": [{"workflow_argument_name": "fastq", "value": {"filename": "SRR5863572_1.fastq.gz", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFINMOVEEF", "display_title": "4DNFINMOVEEF.fastq.gz", "uuid": "168dd42b-b5d7-402b-b977-cc513c8c6e1d", "@id": "/files-fastq/4DNFINMOVEEF/", "status": "released", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "display_title": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"status": "released", "@type": ["Workflow", "Item"], "display_title": "Getting first line of fastq file - 4DNWFASTQFO1", "title": "Getting first line of fastq file", "uuid": "93a1a931-d55d-4623-adfb-0fa735daf6ae", "@id": "/workflows/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": []}