{"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": "3ea753e51f5a0692f5bb30ea582e2314", "status": "released", "aliases": ["4dn-dcic-lab:SRR5339810_2_fq"], "dbxrefs": ["SRA:SRR5339810"], "filename": "SRR5339810_2.fastq.gz", "accession": "4DNFIJMF84XS", "file_size": 8843973588, "file_type": "reads", "instrument": "Illumina HiSeq 2000", "paired_end": "2", "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": "2019-08-12T14:49:51.437218+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2020-04-07T03:39:13.835083+00:00"}, "related_files": [{"file": {"accession": "4DNFIPNRD7SI", "display_title": "4DNFIPNRD7SI.fastq.gz", "@id": "/files-fastq/4DNFIPNRD7SI/", "uuid": "b90f6b74-65e1-4673-ba2b-22ab0eac66eb", "@type": ["FileFastq", "File", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "relationship_type": "paired with"}], "content_md5sum": "1d807b001eb752f9397636f29676e8c6", "public_release": "2019-12-01", "quality_metric": {"@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "overall_quality_status": "PASS", "Total Sequences": 231902756, "display_title": "QualityMetricFastqc from 2019-08-22", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIJMF84XS/fastqc_report.html", "status": "released", "uuid": "88767b90-85c2-492e-a070-ac86a2fbb4dc", "@id": "/quality-metrics-fastqc/88767b90-85c2-492e-a070-ac86a2fbb4dc/", "Sequence length": "48", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "schema_version": "2", "file_first_line": "@HWI-D00175:369:C7MWYANXX:7:1101:1493:2040", "project_release": "2019-12-01", "file_classification": "raw file", "@id": "/files-fastq/4DNFIJMF84XS/", "@type": ["FileFastq", "File", "Item"], "uuid": "5d3e6716-5cc6-4816-a825-e302b6008822", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNFIJMF84XS.fastq.gz", "external_references": [{"ref": "SRA:SRR5339810", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5339810"}], "experiments": [{"status": "released", "display_title": "in situ Hi-C on 46C with Sox1-GFP with DpnII - 4DNEXVBF7QRA", "accession": "4DNEXVBF7QRA", "uuid": "795b09bc-531b-415c-b2aa-819c4abd58ec", "@id": "/experiments-hi-c/4DNEXVBF7QRA/", "@type": ["ExperimentHiC", "Experiment", "Item"], "biosample": {"accession": "4DNBSDU7Y6IR", "modifications_summary": "None", "treatments_summary": "None", "display_title": "4DNBSDU7Y6IR", "uuid": "644732eb-60e7-4c37-add7-b317b9f99065", "@type": ["Biosample", "Item"], "@id": "/biosamples/4DNBSDU7Y6IR/", "biosource_summary": "46C with Sox1-GFP", "status": "released", "biosource": [{"@type": ["Biosource", "Item"], "status": "released", "display_title": "46C with Sox1-GFP - 4DNSRNTW8KVA", "@id": "/biosources/4DNSRNTW8KVA/", "uuid": "15180a95-b2ca-4be7-99b1-7a9f7b2620aa", "override_biosource_name": "46C with Sox1-GFP", "biosource_type": "stem cell derived cell line", "cell_line_tier": "Unclassified", "cell_line": {"@id": "/ontology-terms/EFO:0005484/", "term_id": "EFO:0005484", "term_name": "46C", "@type": ["OntologyTerm", "Item"], "display_title": "46C", "uuid": "1dd66cb6-7900-405f-a7ea-0f88966ca969", "preferred_name": "46C", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "modifications": [{"display_title": "Stable Transfection replacement for Sox1 mouse gene", "status": "released", "uuid": "acd9be42-59e6-4c5b-983d-1a61208cb29d", "genomic_change": "replacement", "modification_type": "Stable Transfection", "@type": ["Modification", "Item"], "@id": "/modifications/acd9be42-59e6-4c5b-983d-1a61208cb29d/", "target_of_mod": [{"@id": "/bio-features/6d5fb946-7a9f-4c67-9cd3-0037862afdc6/", "display_title": "Sox1 mouse gene", "organism_name": "mouse", "uuid": "6d5fb946-7a9f-4c67-9cd3-0037862afdc6", "status": "released", "@type": ["BioFeature", "Item"], "relevant_genes": [{"display_title": "Sox1", "status": "released", "uuid": "017608e0-9f01-4173-ac83-d2a3d99e28bb", "@type": ["Gene", "Item"], "@id": "/genes/20664/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "feature_type": {"@id": "/ontology-terms/SO:0000704/", "status": "released", "display_title": "gene", "@type": ["OntologyTerm", "Item"], "uuid": "0231da78-1adc-4b8a-89b9-4f91908412a3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "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/4DNINES2PTTN/", "@type": ["IndividualMouse", "Individual", "Item"], "uuid": "fb69d05b-0e11-4d5e-bace-a9767f9c9e81", "status": "released", "display_title": "4DNINES2PTTN", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "cell_culture_details": [{"@type": ["BiosampleCellCulture", "Item"], "status": "released", "display_title": "BiosampleCellCulture from 2019-08-12", "uuid": "b178bdb4-00e3-42f8-af47-89c924d49716", "@id": "/biosample-cell-cultures/b178bdb4-00e3-42f8-af47-89c924d49716/", "in_vitro_differentiated": "Yes", "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/4DNESJ9SIAV5/", "display_title": "4DNESJ9SIAV5", "accession": "4DNESJ9SIAV5", "uuid": "458e5476-8946-4820-af50-95c25fff73b2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "last_modified": {"date_modified": "2019-12-01T23:01:25.500760+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 3, Techrep 1", "biosource_name": "46C with Sox1-GFP", "lab_name": "Giacomo Cavalli, UM"}, "title": "4DNFIJMF84XS", "href": "/files-fastq/4DNFIJMF84XS/@@download/4DNFIJMF84XS.fastq.gz", "upload_key": "5d3e6716-5cc6-4816-a825-e302b6008822/4DNFIJMF84XS.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/5d3e6716-5cc6-4816-a825-e302b6008822/4DNFIJMF84XS.fastq.gz", "tsv_notes": "", "workflow_run_inputs": [{"display_title": "md5 0.2.6 run 2019-08-21 23:12:44.329649", "@id": "/workflow-runs-awsem/93043ca3-5b58-47a7-9302-d9cf9845ea53/", "uuid": "93043ca3-5b58-47a7-9302-d9cf9845ea53", "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/4DNFIJMF84XS/", "uuid": "5d3e6716-5cc6-4816-a825-e302b6008822", "filename": "SRR5339810_2.fastq.gz", "accession": "4DNFIJMF84XS", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIJMF84XS.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 2019-08-22 00:28:41.745656", "@id": "/workflow-runs-awsem/9ad8e36f-3747-473b-b74a-8ca8d8fd48e2/", "uuid": "9ad8e36f-3747-473b-b74a-8ca8d8fd48e2", "status": "released", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "output_files": [{"workflow_argument_name": "report_zip", "value_qc": {"@id": "/quality-metrics-fastqc/88767b90-85c2-492e-a070-ac86a2fbb4dc/", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIJMF84XS/fastqc_report.html", "uuid": "88767b90-85c2-492e-a070-ac86a2fbb4dc", "display_title": "QualityMetricFastqc from 2019-08-22", "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/4DNFIJMF84XS/", "uuid": "5d3e6716-5cc6-4816-a825-e302b6008822", "filename": "SRR5339810_2.fastq.gz", "accession": "4DNFIJMF84XS", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIJMF84XS.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 03:06:16.675014", "@id": "/workflow-runs-awsem/d41cea27-0cf4-402a-b9cc-4e2fc18463b8/", "uuid": "d41cea27-0cf4-402a-b9cc-4e2fc18463b8", "status": "released", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "output_files": [{"workflow_argument_name": "out_bam", "value": {"accession": "4DNFIHIMI4NU", "uuid": "3a6e04b3-8c0a-48da-9738-f8d44f61611d", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIHIMI4NU.bam", "status": "released", "@id": "/files-processed/4DNFIHIMI4NU/", "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/4DNFIPNRD7SI/", "uuid": "b90f6b74-65e1-4673-ba2b-22ab0eac66eb", "filename": "SRR5339810_1.fastq.gz", "accession": "4DNFIPNRD7SI", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIPNRD7SI.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/4DNFIJMF84XS/", "uuid": "5d3e6716-5cc6-4816-a825-e302b6008822", "filename": "SRR5339810_2.fastq.gz", "accession": "4DNFIJMF84XS", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIJMF84XS.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 2020-04-07 03:34:02.893215", "@id": "/workflow-runs-awsem/f2caa8a0-9a65-4997-9a23-75c8b6a02c6a/", "uuid": "f2caa8a0-9a65-4997-9a23-75c8b6a02c6a", "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/4DNFIJMF84XS/", "uuid": "5d3e6716-5cc6-4816-a825-e302b6008822", "filename": "SRR5339810_2.fastq.gz", "accession": "4DNFIJMF84XS", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIJMF84XS.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": []}