{"lab": {"@type": ["Lab", "Item"], "@id": "/labs/giacomo-cavalli-lab/", "status": "current", "title": "Giacomo Cavalli, UM", "display_title": "Giacomo Cavalli, UM", "uuid": "c38cf2e8-1129-48e1-b8a4-d42e88258e30", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.c38cf2e8-1129-48e1-b8a4-d42e88258e30"]}}, "award": {"center": "External", "center_title": "External", "project": "External", "description": "Funding source is from outside 4DN.", "@id": "/awards/external-award/", "status": "current", "display_title": "EXTERNAL AWARD", "name": "external-award", "uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "@type": ["Award", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "eb1d2d36c8d5c24af0a66c3b25bf3380", "status": "released", "aliases": ["4dn-dcic-lab:SRR5339828_1_fq"], "dbxrefs": ["SRA:SRR5339828"], "filename": "SRR5339828_1.fastq.gz", "accession": "4DNFIX5M35WV", "file_size": 11220206880, "file_type": "reads", "instrument": "Illumina HiSeq 2000", "paired_end": "1", "file_format": {"status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "file_format": "fastq", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "read_length": 49, "date_created": "2019-08-12T14:50:23.524381+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2020-04-07T03:35:06.011084+00:00"}, "related_files": [{"file": {"accession": "4DNFIFNMB6K6", "uuid": "319a5d43-1300-49eb-ba35-09204ac79d64", "display_title": "4DNFIFNMB6K6.fastq.gz", "@type": ["FileFastq", "File", "Item"], "status": "released", "@id": "/files-fastq/4DNFIFNMB6K6/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "relationship_type": "paired with"}], "content_md5sum": "44f3a7143a10f34ccfbd05b30c6c3264", "public_release": "2019-12-01", "quality_metric": {"display_title": "QualityMetricFastqc from 2019-08-20", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "30f86510-a689-4d78-8cd0-29536f9f7a76", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIX5M35WVqc_report.html", "status": "released", "overall_quality_status": "PASS", "Total Sequences": 272017744, "Sequence length": "50", "@id": "/quality-metrics-fastqc/30f86510-a689-4d78-8cd0-29536f9f7a76/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "schema_version": "2", "file_first_line": "@HISEQ:403:C864DANXX:6:1101:6123:33942", "project_release": "2019-12-01", "file_classification": "raw file", "@id": "/files-fastq/4DNFIX5M35WV/", "@type": ["FileFastq", "File", "Item"], "uuid": "00103f72-a571-4ed8-96c9-20dac1c37df7", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNFIX5M35WV.fastq.gz", "external_references": [{"ref": "SRA:SRR5339828", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5339828"}], "experiments": [{"@id": "/experiments-hi-c/4DNEXYY2LOHJ/", "uuid": "40ccbc73-3d3d-4b8b-abb2-272a01cb8092", "@type": ["ExperimentHiC", "Experiment", "Item"], "display_title": "in situ Hi-C on 46C with Sox1-GFP with DpnII - 4DNEXYY2LOHJ", "status": "released", "accession": "4DNEXYY2LOHJ", "experiment_type": {"@id": "/experiment-types/in-situ-hi-c/", "status": "released", "@type": ["ExperimentType", "Item"], "display_title": "in situ Hi-C", "uuid": "a2920a38-cdba-4ff0-b4f0-c6bb53257747", "title": "in situ Hi-C", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "biosample": {"@type": ["Biosample", "Item"], "display_title": "4DNBSMW9D9G9", "status": "released", "uuid": "910d420f-1977-4507-b476-601535b60181", "@id": "/biosamples/4DNBSMW9D9G9/", "accession": "4DNBSMW9D9G9", "modifications_summary": "None", "treatments_summary": "None", "biosource_summary": "46C with Sox1-GFP", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "biosource": [{"@type": ["Biosource", "Item"], "status": "released", "biosource_type": "stem cell derived cell line", "display_title": "46C with Sox1-GFP - 4DNSRNTW8KVA", "uuid": "15180a95-b2ca-4be7-99b1-7a9f7b2620aa", "@id": "/biosources/4DNSRNTW8KVA/", "override_biosource_name": "46C with Sox1-GFP", "cell_line_tier": "Unclassified", "modifications": [{"uuid": "acd9be42-59e6-4c5b-983d-1a61208cb29d", "status": "released", "@type": ["Modification", "Item"], "@id": "/modifications/acd9be42-59e6-4c5b-983d-1a61208cb29d/", "display_title": "Stable Transfection replacement for Sox1 mouse gene", "genomic_change": "replacement", "modification_type": "Stable Transfection", "target_of_mod": [{"display_title": "Sox1 mouse gene", "organism_name": "mouse", "@id": "/bio-features/6d5fb946-7a9f-4c67-9cd3-0037862afdc6/", "status": "released", "@type": ["BioFeature", "Item"], "uuid": "6d5fb946-7a9f-4c67-9cd3-0037862afdc6", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "relevant_genes": [{"uuid": "017608e0-9f01-4173-ac83-d2a3d99e28bb", "@id": "/genes/20664/", "@type": ["Gene", "Item"], "status": "released", "display_title": "Sox1", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "feature_type": {"@id": "/ontology-terms/SO:0000704/", "@type": ["OntologyTerm", "Item"], "display_title": "gene", "status": "released", "uuid": "0231da78-1adc-4b8a-89b9-4f91908412a3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "organism": {"status": "released", "name": "mouse", "@id": "/organisms/10090/", "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "@type": ["Organism", "Item"], "display_title": "M. musculus", "scientific_name": "Mus musculus", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "cell_line": {"preferred_name": "46C", "@type": ["OntologyTerm", "Item"], "term_name": "46C", "display_title": "46C", "@id": "/ontology-terms/EFO:0005484/", "uuid": "1dd66cb6-7900-405f-a7ea-0f88966ca969", "term_id": "EFO:0005484", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"@type": ["OntologyTerm", "Item"], "status": "released", "term_name": "stem cell", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "term_id": "CL:0000034", "preferred_name": "stem cell", "@id": "/ontology-terms/CL:0000034/", "display_title": "stem cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"@id": "/individuals-mouse/4DNINES2PTTN/", "@type": ["IndividualMouse", "Individual", "Item"], "display_title": "4DNINES2PTTN", "uuid": "fb69d05b-0e11-4d5e-bace-a9767f9c9e81", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "cell_culture_details": [{"status": "released", "in_vitro_differentiated": "Yes", "@type": ["BiosampleCellCulture", "Item"], "uuid": "345928f0-d02d-4dab-a794-21e35540ed82", "@id": "/biosample-cell-cultures/345928f0-d02d-4dab-a794-21e35540ed82/", "display_title": "BiosampleCellCulture from 2019-08-12", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, "digestion_enzyme": {"uuid": "356a57a1-1f1d-463d-a972-27742f79a6a5", "display_title": "DpnII", "@type": ["Enzyme", "Item"], "status": "released", "@id": "/enzymes/DpnII/", "name": "DpnII", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_sets": [{"experimentset_type": "replicate", "@id": "/experiment-set-replicates/4DNESJ9SIAV5/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "458e5476-8946-4820-af50-95c25fff73b2", "accession": "4DNESJ9SIAV5", "status": "released", "display_title": "4DNESJ9SIAV5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2019-12-01T23:01:39.107090+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 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": "4DNFIX5M35WV", "href": "/files-fastq/4DNFIX5M35WV/@@download/4DNFIX5M35WV.fastq.gz", "upload_key": "00103f72-a571-4ed8-96c9-20dac1c37df7/4DNFIX5M35WV.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/00103f72-a571-4ed8-96c9-20dac1c37df7/4DNFIX5M35WV.fastq.gz", "tsv_notes": "", "workflow_run_inputs": [{"display_title": "md5 0.2.6 run 2019-08-20 21:35:40.542918", "@id": "/workflow-runs-awsem/2aa25d69-2e20-4e0a-9f80-275d7a5d36ca/", "status": "released", "uuid": "2aa25d69-2e20-4e0a-9f80-275d7a5d36ca", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "output_files": [{"workflow_argument_name": "report"}], "input_files": [{"workflow_argument_name": "input_file", "value": {"accession": "4DNFIX5M35WV", "filename": "SRR5339828_1.fastq.gz", "display_title": "4DNFIX5M35WV.fastq.gz", "@id": "/files-fastq/4DNFIX5M35WV/", "@type": ["FileFastq", "File", "Item"], "status": "released", "uuid": "00103f72-a571-4ed8-96c9-20dac1c37df7", "file_format": {"display_title": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"title": "md5 0.2.6", "display_title": "md5 0.2.6 - 4DNWF2HFF82B", "@id": "/workflows/4DNWF2HFF82B/", "uuid": "c77a117b-9a58-477e-aaa5-291a109a99f6", "@type": ["Workflow", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "fastqc v1 run 2019-08-20 21:35:44.233472", "@id": "/workflow-runs-awsem/8e07b282-fa34-4429-a84c-1d0d248895c1/", "status": "released", "uuid": "8e07b282-fa34-4429-a84c-1d0d248895c1", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "output_files": [{"workflow_argument_name": "report_zip", "value_qc": {"display_title": "QualityMetricFastqc from 2019-08-20", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIX5M35WVqc_report.html", "status": "released", "uuid": "30f86510-a689-4d78-8cd0-29536f9f7a76", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/30f86510-a689-4d78-8cd0-29536f9f7a76/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "input_files": [{"workflow_argument_name": "input_fastq", "value": {"accession": "4DNFIX5M35WV", "filename": "SRR5339828_1.fastq.gz", "display_title": "4DNFIX5M35WV.fastq.gz", "@id": "/files-fastq/4DNFIX5M35WV/", "@type": ["FileFastq", "File", "Item"], "status": "released", "uuid": "00103f72-a571-4ed8-96c9-20dac1c37df7", "file_format": {"display_title": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"title": "FastQC v1", "display_title": "FastQC v1 - 4DNWFAW5VTA5", "@id": "/workflows/4DNWFAW5VTA5/", "uuid": "2324ad76-ff37-4157-8bcc-3ce72b7dace9", "@type": ["Workflow", "Item"], "status": "released", "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 04:03:17.046602", "@id": "/workflow-runs-awsem/803fe3cb-6dcd-4f99-84cf-75bfd9161981/", "status": "released", "uuid": "803fe3cb-6dcd-4f99-84cf-75bfd9161981", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "output_files": [{"workflow_argument_name": "out_bam", "value": {"status": "released", "uuid": "243d4e4f-edc2-4bab-8667-753e812e77bb", "display_title": "4DNFIFFOPWSK.bam", "@id": "/files-processed/4DNFIFFOPWSK/", "accession": "4DNFIFFOPWSK", "@type": ["FileProcessed", "File", "Item"], "file_format": {"status": "released", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "file_format": "bam", "display_title": "bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "input_files": [{"workflow_argument_name": "bwa_index", "value": {"accession": "4DNFI823LSI8", "filename": "mm10.bwaIndex.tgz", "display_title": "4DNFI823LSI8.bwaIndex.tgz", "@id": "/files-reference/4DNFI823LSI8/", "@type": ["FileReference", "File", "Item"], "status": "released", "uuid": "4a6d10ee-2edb-4402-a98f-0edb1d58f5e1", "file_format": {"display_title": "bwaIndex", "status": "released", "@type": ["FileFormat", "Item"], "file_format": "bwaIndex", "uuid": "d13d06cf-218e-4f61-55f0-91f226248b2c", "@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": {"accession": "4DNFIX5M35WV", "filename": "SRR5339828_1.fastq.gz", "display_title": "4DNFIX5M35WV.fastq.gz", "@id": "/files-fastq/4DNFIX5M35WV/", "@type": ["FileFastq", "File", "Item"], "status": "released", "uuid": "00103f72-a571-4ed8-96c9-20dac1c37df7", "file_format": {"display_title": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@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": {"accession": "4DNFIFNMB6K6", "filename": "SRR5339828_2.fastq.gz", "display_title": "4DNFIFNMB6K6.fastq.gz", "@id": "/files-fastq/4DNFIFNMB6K6/", "@type": ["FileFastq", "File", "Item"], "status": "released", "uuid": "319a5d43-1300-49eb-ba35-09204ac79d64", "file_format": {"display_title": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"title": "Alignment for Hi-C using bwa-mem 0.2.6", "display_title": "Alignment for Hi-C using bwa-mem 0.2.6 - 4DNWF84NFOQP", "@id": "/workflows/4DNWF84NFOQP/", "uuid": "3feedadc-50f9-4bb4-919b-09a8b731d0cc", "@type": ["Workflow", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "fastq-first-line v2 run 2020-04-07 03:29:55.023355", "@id": "/workflow-runs-awsem/69c9aceb-2f7d-4041-b3f4-6ba2cb31fb90/", "status": "released", "uuid": "69c9aceb-2f7d-4041-b3f4-6ba2cb31fb90", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "output_files": [{"workflow_argument_name": "first_line"}], "input_files": [{"workflow_argument_name": "fastq", "value": {"accession": "4DNFIX5M35WV", "filename": "SRR5339828_1.fastq.gz", "display_title": "4DNFIX5M35WV.fastq.gz", "@id": "/files-fastq/4DNFIX5M35WV/", "@type": ["FileFastq", "File", "Item"], "status": "released", "uuid": "00103f72-a571-4ed8-96c9-20dac1c37df7", "file_format": {"display_title": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"title": "Getting first line of fastq file", "display_title": "Getting first line of fastq file - 4DNWFASTQFO1", "@id": "/workflows/4DNWFASTQFO1/", "uuid": "93a1a931-d55d-4623-adfb-0fa735daf6ae", "@type": ["Workflow", "Item"], "status": "released", "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": []}