{"lab": {"status": "current", "display_title": "Giacomo Cavalli, UM", "uuid": "c38cf2e8-1129-48e1-b8a4-d42e88258e30", "title": "Giacomo Cavalli, UM", "@id": "/labs/giacomo-cavalli-lab/", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.c38cf2e8-1129-48e1-b8a4-d42e88258e30"]}}, "award": {"status": "current", "name": "external-award", "description": "Funding source is from outside 4DN.", "@id": "/awards/external-award/", "center_title": "External", "uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "@type": ["Award", "Item"], "project": "External", "display_title": "EXTERNAL AWARD", "center": "External", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "6f1f4331195d7e3109cbeb445a9783b5", "status": "released", "aliases": ["4dn-dcic-lab:SRR5339815_2_fq"], "dbxrefs": ["SRA:SRR5339815"], "filename": "SRR5339815_2.fastq.gz", "accession": "4DNFIENIFKUI", "file_size": 1863431118, "file_type": "reads", "instrument": "Illumina HiSeq 2000", "paired_end": "2", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "display_title": "fastq", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "read_length": 49, "date_created": "2019-08-12T14:50:06.461829+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2020-04-07T03:38:03.473191+00:00"}, "related_files": [{"file": {"@type": ["FileFastq", "File", "Item"], "status": "released", "uuid": "68586f02-ad08-4255-8990-ddf8157b185a", "display_title": "4DNFIZXOZNMJ.fastq.gz", "accession": "4DNFIZXOZNMJ", "@id": "/files-fastq/4DNFIZXOZNMJ/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "relationship_type": "paired with"}], "content_md5sum": "cd9b1cd9c99348495b995db5bd6113d3", "public_release": "2019-12-01", "quality_metric": {"@id": "/quality-metrics-fastqc/ca22f7bf-a7af-4dc3-8406-64378def04fa/", "uuid": "ca22f7bf-a7af-4dc3-8406-64378def04fa", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "overall_quality_status": "PASS", "status": "released", "Sequence length": "48", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIENIFKUI/fastqc_report.html", "display_title": "QualityMetricFastqc from 2019-08-20", "Total Sequences": 45016917, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "schema_version": "2", "file_first_line": "@HISEQ:365:C71NAANXX:1:1101:1457:1980", "project_release": "2019-12-01", "file_classification": "raw file", "@id": "/files-fastq/4DNFIENIFKUI/", "@type": ["FileFastq", "File", "Item"], "uuid": "45e20dca-220a-4a5e-983f-d31de988c5a6", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNFIENIFKUI.fastq.gz", "external_references": [{"ref": "SRA:SRR5339815", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5339815"}], "experiments": [{"display_title": "in situ Hi-C on 46C with Sox1-GFP with DpnII - 4DNEXYY2LOHJ", "status": "released", "@id": "/experiments-hi-c/4DNEXYY2LOHJ/", "@type": ["ExperimentHiC", "Experiment", "Item"], "accession": "4DNEXYY2LOHJ", "uuid": "40ccbc73-3d3d-4b8b-abb2-272a01cb8092", "biosample": {"biosource_summary": "46C with Sox1-GFP", "@type": ["Biosample", "Item"], "uuid": "910d420f-1977-4507-b476-601535b60181", "@id": "/biosamples/4DNBSMW9D9G9/", "status": "released", "modifications_summary": "None", "display_title": "4DNBSMW9D9G9", "accession": "4DNBSMW9D9G9", "treatments_summary": "None", "biosource": [{"biosource_type": "stem cell derived cell line", "cell_line_tier": "Unclassified", "status": "released", "@id": "/biosources/4DNSRNTW8KVA/", "@type": ["Biosource", "Item"], "uuid": "15180a95-b2ca-4be7-99b1-7a9f7b2620aa", "display_title": "46C with Sox1-GFP - 4DNSRNTW8KVA", "override_biosource_name": "46C with Sox1-GFP", "modifications": [{"@id": "/modifications/acd9be42-59e6-4c5b-983d-1a61208cb29d/", "display_title": "Stable Transfection replacement for Sox1 mouse gene", "status": "released", "uuid": "acd9be42-59e6-4c5b-983d-1a61208cb29d", "modification_type": "Stable Transfection", "@type": ["Modification", "Item"], "genomic_change": "replacement", "target_of_mod": [{"status": "released", "organism_name": "mouse", "display_title": "Sox1 mouse gene", "uuid": "6d5fb946-7a9f-4c67-9cd3-0037862afdc6", "@id": "/bio-features/6d5fb946-7a9f-4c67-9cd3-0037862afdc6/", "@type": ["BioFeature", "Item"], "relevant_genes": [{"uuid": "017608e0-9f01-4173-ac83-d2a3d99e28bb", "status": "released", "@type": ["Gene", "Item"], "display_title": "Sox1", "@id": "/genes/20664/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "feature_type": {"@id": "/ontology-terms/SO:0000704/", "uuid": "0231da78-1adc-4b8a-89b9-4f91908412a3", "display_title": "gene", "status": "released", "@type": ["OntologyTerm", "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"]}}], "tissue": {"term_name": "stem cell", "preferred_name": "stem cell", "@type": ["OntologyTerm", "Item"], "term_id": "CL:0000034", "display_title": "stem cell", "status": "released", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "@id": "/ontology-terms/CL:0000034/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "cell_line": {"display_title": "46C", "preferred_name": "46C", "@id": "/ontology-terms/EFO:0005484/", "status": "released", "term_name": "46C", "uuid": "1dd66cb6-7900-405f-a7ea-0f88966ca969", "@type": ["OntologyTerm", "Item"], "term_id": "EFO:0005484", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"status": "released", "scientific_name": "Mus musculus", "name": "mouse", "display_title": "M. musculus", "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "@type": ["Organism", "Item"], "@id": "/organisms/10090/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"@type": ["IndividualMouse", "Individual", "Item"], "display_title": "4DNINES2PTTN", "status": "released", "uuid": "fb69d05b-0e11-4d5e-bace-a9767f9c9e81", "@id": "/individuals-mouse/4DNINES2PTTN/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "cell_culture_details": [{"in_vitro_differentiated": "Yes", "@type": ["BiosampleCellCulture", "Item"], "display_title": "BiosampleCellCulture from 2019-08-12", "@id": "/biosample-cell-cultures/345928f0-d02d-4dab-a794-21e35540ed82/", "uuid": "345928f0-d02d-4dab-a794-21e35540ed82", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "digestion_enzyme": {"display_title": "DpnII", "@type": ["Enzyme", "Item"], "status": "released", "@id": "/enzymes/DpnII/", "uuid": "356a57a1-1f1d-463d-a972-27742f79a6a5", "name": "DpnII", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2019-12-01T23:01:39.107090+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "experiment_type": {"title": "in situ Hi-C", "@type": ["ExperimentType", "Item"], "display_title": "in situ Hi-C", "uuid": "a2920a38-cdba-4ff0-b4f0-c6bb53257747", "status": "released", "@id": "/experiment-types/in-situ-hi-c/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_sets": [{"status": "released", "uuid": "458e5476-8946-4820-af50-95c25fff73b2", "display_title": "4DNESJ9SIAV5", "experimentset_type": "replicate", "accession": "4DNESJ9SIAV5", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "@id": "/experiment-set-replicates/4DNESJ9SIAV5/", "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 mESC during neural differentiation", "condition": "G0G1 neural progenitors cells  (FACS sorted, Sox1-GFP+)", "replicate_info": "Biorep 4, Techrep 1", "biosource_name": "46C with Sox1-GFP", "lab_name": "Giacomo Cavalli, UM"}, "title": "4DNFIENIFKUI", "href": "/files-fastq/4DNFIENIFKUI/@@download/4DNFIENIFKUI.fastq.gz", "upload_key": "45e20dca-220a-4a5e-983f-d31de988c5a6/4DNFIENIFKUI.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/45e20dca-220a-4a5e-983f-d31de988c5a6/4DNFIENIFKUI.fastq.gz", "tsv_notes": "", "workflow_run_inputs": [{"@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "uuid": "a1b5e2e7-a5c0-4a46-9c28-46f852dd3c06", "status": "released", "@id": "/workflow-runs-awsem/a1b5e2e7-a5c0-4a46-9c28-46f852dd3c06/", "display_title": "fastqc v1 run 2019-08-20 21:38:31.265741", "input_files": [{"workflow_argument_name": "input_fastq", "value": {"status": "released", "uuid": "45e20dca-220a-4a5e-983f-d31de988c5a6", "accession": "4DNFIENIFKUI", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIENIFKUI.fastq.gz", "filename": "SRR5339815_2.fastq.gz", "@id": "/files-fastq/4DNFIENIFKUI/", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "fastq", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"display_title": "FastQC v1 - 4DNWFAW5VTA5", "uuid": "2324ad76-ff37-4157-8bcc-3ce72b7dace9", "status": "released", "title": "FastQC v1", "@id": "/workflows/4DNWFAW5VTA5/", "@type": ["Workflow", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "output_files": [{"workflow_argument_name": "report_zip", "value_qc": {"uuid": "ca22f7bf-a7af-4dc3-8406-64378def04fa", "status": "released", "@id": "/quality-metrics-fastqc/ca22f7bf-a7af-4dc3-8406-64378def04fa/", "overall_quality_status": "PASS", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIENIFKUI/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "display_title": "QualityMetricFastqc from 2019-08-20", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "uuid": "3acf027e-9977-4ca3-a5f7-75295221e241", "status": "released", "@id": "/workflow-runs-awsem/3acf027e-9977-4ca3-a5f7-75295221e241/", "display_title": "md5 0.2.6 run 2019-08-20 21:38:22.163077", "input_files": [{"workflow_argument_name": "input_file", "value": {"status": "released", "uuid": "45e20dca-220a-4a5e-983f-d31de988c5a6", "accession": "4DNFIENIFKUI", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIENIFKUI.fastq.gz", "filename": "SRR5339815_2.fastq.gz", "@id": "/files-fastq/4DNFIENIFKUI/", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "fastq", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"display_title": "md5 0.2.6 - 4DNWF2HFF82B", "uuid": "c77a117b-9a58-477e-aaa5-291a109a99f6", "status": "released", "title": "md5 0.2.6", "@id": "/workflows/4DNWF2HFF82B/", "@type": ["Workflow", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "output_files": [{"workflow_argument_name": "report"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "uuid": "52a88619-909f-44bd-b1ad-9db0b262ef35", "status": "released", "@id": "/workflow-runs-awsem/52a88619-909f-44bd-b1ad-9db0b262ef35/", "display_title": "bwa-mem 0.2.6 run 2019-10-16 03:06:42.226947", "input_files": [{"workflow_argument_name": "bwa_index", "value": {"status": "released", "uuid": "4a6d10ee-2edb-4402-a98f-0edb1d58f5e1", "accession": "4DNFI823LSI8", "@type": ["FileReference", "File", "Item"], "display_title": "4DNFI823LSI8.bwaIndex.tgz", "filename": "mm10.bwaIndex.tgz", "@id": "/files-reference/4DNFI823LSI8/", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bwaIndex", "@id": "/file-formats/bwaIndex/", "uuid": "d13d06cf-218e-4f61-55f0-91f226248b2c", "status": "released", "file_format": "bwaIndex", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "fastq1", "value": {"status": "released", "uuid": "68586f02-ad08-4255-8990-ddf8157b185a", "accession": "4DNFIZXOZNMJ", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIZXOZNMJ.fastq.gz", "filename": "SRR5339815_1.fastq.gz", "@id": "/files-fastq/4DNFIZXOZNMJ/", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "fastq", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "fastq2", "value": {"status": "released", "uuid": "45e20dca-220a-4a5e-983f-d31de988c5a6", "accession": "4DNFIENIFKUI", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIENIFKUI.fastq.gz", "filename": "SRR5339815_2.fastq.gz", "@id": "/files-fastq/4DNFIENIFKUI/", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "fastq", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"display_title": "Alignment for Hi-C using bwa-mem 0.2.6 - 4DNWF84NFOQP", "uuid": "3feedadc-50f9-4bb4-919b-09a8b731d0cc", "status": "released", "title": "Alignment for Hi-C using bwa-mem 0.2.6", "@id": "/workflows/4DNWF84NFOQP/", "@type": ["Workflow", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "output_files": [{"workflow_argument_name": "out_bam", "value": {"status": "released", "accession": "4DNFIE7NSRDP", "@id": "/files-processed/4DNFIE7NSRDP/", "uuid": "e5155b96-4d10-479a-9226-6e375d7387f3", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIE7NSRDP.bam", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "file_format": "bam", "@id": "/file-formats/bam/", "@type": ["FileFormat", "Item"], "display_title": "bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "uuid": "608e6765-ba68-4972-bd99-7f7cee5c253b", "status": "released", "@id": "/workflow-runs-awsem/608e6765-ba68-4972-bd99-7f7cee5c253b/", "display_title": "fastq-first-line v2 run 2020-04-07 03:32:52.725593", "input_files": [{"workflow_argument_name": "fastq", "value": {"status": "released", "uuid": "45e20dca-220a-4a5e-983f-d31de988c5a6", "accession": "4DNFIENIFKUI", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIENIFKUI.fastq.gz", "filename": "SRR5339815_2.fastq.gz", "@id": "/files-fastq/4DNFIENIFKUI/", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "fastq", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"display_title": "Getting first line of fastq file - 4DNWFASTQFO1", "uuid": "93a1a931-d55d-4623-adfb-0fa735daf6ae", "status": "released", "title": "Getting first line of fastq file", "@id": "/workflows/4DNWFASTQFO1/", "@type": ["Workflow", "Item"], "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": []}