{"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": "8e943fd5553d397a20b2a9707aca33aa", "status": "released", "aliases": ["4dn-dcic-lab:SRR5339787_1_fq"], "dbxrefs": ["SRA:SRR5339787"], "filename": "SRR5339787_1.fastq.gz", "accession": "4DNFITRH621N", "file_size": 7873905601, "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": "2019-08-12T14:48:40.136737+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2020-04-07T03:44:45.331545+00:00"}, "related_files": [{"file": {"accession": "4DNFI31PQGVP", "uuid": "c877bc21-8278-46e1-8f9a-aa6b26ed4c02", "display_title": "4DNFI31PQGVP.fastq.gz", "@type": ["FileFastq", "File", "Item"], "status": "released", "@id": "/files-fastq/4DNFI31PQGVP/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "relationship_type": "paired with"}], "content_md5sum": "b61602552f3c4ff9eada836ab577b0c1", "public_release": "2019-12-01", "quality_metric": {"display_title": "QualityMetricFastqc from 2019-08-15", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "bc0d06d9-c4c5-4430-8954-3c1e44022f61", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFITRH621N/fastqc_report.html", "status": "released", "overall_quality_status": "PASS", "Total Sequences": 209058864, "Sequence length": "50", "@id": "/quality-metrics-fastqc/bc0d06d9-c4c5-4430-8954-3c1e44022f61/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "schema_version": "2", "file_first_line": "@HWI-D00175:367:C7J0HANXX:8:1101:16607:43302", "project_release": "2019-12-01", "file_classification": "raw file", "@id": "/files-fastq/4DNFITRH621N/", "@type": ["FileFastq", "File", "Item"], "uuid": "0f9fc037-00aa-4b3b-be63-5c4b3b849f87", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNFITRH621N.fastq.gz", "external_references": [{"ref": "SRA:SRR5339787", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5339787"}], "experiments": [{"@id": "/experiments-hi-c/4DNEXOPQXJ3G/", "uuid": "84fbb4a7-a2c4-430c-b31b-b7e589b38522", "@type": ["ExperimentHiC", "Experiment", "Item"], "display_title": "in situ Hi-C on 46C with Sox1-GFP with DpnII - 4DNEXOPQXJ3G", "status": "released", "accession": "4DNEXOPQXJ3G", "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": "4DNBSSJVS4TJ", "status": "released", "uuid": "5e04695a-b5e8-4348-8660-56a1ada8911b", "@id": "/biosamples/4DNBSSJVS4TJ/", "accession": "4DNBSSJVS4TJ", "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": "bd7e9468-ca7e-4beb-a98e-8d41b82742ca", "@id": "/biosample-cell-cultures/bd7e9468-ca7e-4beb-a98e-8d41b82742ca/", "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": "2019-12-01T23:01:23.584942+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 1, Techrep 1", "biosource_name": "46C with Sox1-GFP", "lab_name": "Giacomo Cavalli, UM"}, "title": "4DNFITRH621N", "href": "/files-fastq/4DNFITRH621N/@@download/4DNFITRH621N.fastq.gz", "upload_key": "0f9fc037-00aa-4b3b-be63-5c4b3b849f87/4DNFITRH621N.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/0f9fc037-00aa-4b3b-be63-5c4b3b849f87/4DNFITRH621N.fastq.gz", "tsv_notes": "", "workflow_run_inputs": [{"display_title": "md5 0.2.6 run 2019-08-15 17:37:11.554150", "@id": "/workflow-runs-awsem/b8b81ba7-e049-4be8-8f00-ff9f9db1b729/", "status": "released", "uuid": "b8b81ba7-e049-4be8-8f00-ff9f9db1b729", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "output_files": [{"workflow_argument_name": "report"}], "input_files": [{"workflow_argument_name": "input_file", "value": {"accession": "4DNFITRH621N", "filename": "SRR5339787_1.fastq.gz", "display_title": "4DNFITRH621N.fastq.gz", "@id": "/files-fastq/4DNFITRH621N/", "@type": ["FileFastq", "File", "Item"], "status": "released", "uuid": "0f9fc037-00aa-4b3b-be63-5c4b3b849f87", "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 2019-08-15 17:37:14.911935", "@id": "/workflow-runs-awsem/14eff9e0-6dd9-4418-81a6-28ca97bdf58e/", "status": "released", "uuid": "14eff9e0-6dd9-4418-81a6-28ca97bdf58e", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "output_files": [{"workflow_argument_name": "report_zip", "value_qc": {"display_title": "QualityMetricFastqc from 2019-08-15", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFITRH621N/fastqc_report.html", "status": "released", "uuid": "bc0d06d9-c4c5-4430-8954-3c1e44022f61", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/bc0d06d9-c4c5-4430-8954-3c1e44022f61/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "input_files": [{"workflow_argument_name": "input_fastq", "value": {"accession": "4DNFITRH621N", "filename": "SRR5339787_1.fastq.gz", "display_title": "4DNFITRH621N.fastq.gz", "@id": "/files-fastq/4DNFITRH621N/", "@type": ["FileFastq", "File", "Item"], "status": "released", "uuid": "0f9fc037-00aa-4b3b-be63-5c4b3b849f87", "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 03:04:18.331412", "@id": "/workflow-runs-awsem/e9988b85-bf10-4a60-92ab-4d5a3c1512a0/", "status": "released", "uuid": "e9988b85-bf10-4a60-92ab-4d5a3c1512a0", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "output_files": [{"workflow_argument_name": "out_bam", "value": {"status": "released", "uuid": "9bf714df-ac8d-49f3-9b8c-a785d7619de9", "display_title": "4DNFIT2LGQA1.bam", "@id": "/files-processed/4DNFIT2LGQA1/", "accession": "4DNFIT2LGQA1", "@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": "4DNFITRH621N", "filename": "SRR5339787_1.fastq.gz", "display_title": "4DNFITRH621N.fastq.gz", "@id": "/files-fastq/4DNFITRH621N/", "@type": ["FileFastq", "File", "Item"], "status": "released", "uuid": "0f9fc037-00aa-4b3b-be63-5c4b3b849f87", "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": "4DNFI31PQGVP", "filename": "SRR5339787_2.fastq.gz", "display_title": "4DNFI31PQGVP.fastq.gz", "@id": "/files-fastq/4DNFI31PQGVP/", "@type": ["FileFastq", "File", "Item"], "status": "released", "uuid": "c877bc21-8278-46e1-8f9a-aa6b26ed4c02", "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 03:39:35.053537", "@id": "/workflow-runs-awsem/25ba2fe2-48d8-405f-b548-f25e50cb9f6a/", "status": "released", "uuid": "25ba2fe2-48d8-405f-b548-f25e50cb9f6a", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "output_files": [{"workflow_argument_name": "first_line"}], "input_files": [{"workflow_argument_name": "fastq", "value": {"accession": "4DNFITRH621N", "filename": "SRR5339787_1.fastq.gz", "display_title": "4DNFITRH621N.fastq.gz", "@id": "/files-fastq/4DNFITRH621N/", "@type": ["FileFastq", "File", "Item"], "status": "released", "uuid": "0f9fc037-00aa-4b3b-be63-5c4b3b849f87", "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": []}