{"lab": {"title": "Giacomo Cavalli, UM", "@type": ["Lab", "Item"], "@id": "/labs/giacomo-cavalli-lab/", "uuid": "c38cf2e8-1129-48e1-b8a4-d42e88258e30", "display_title": "Giacomo Cavalli, UM", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.c38cf2e8-1129-48e1-b8a4-d42e88258e30"]}}, "award": {"display_title": "EXTERNAL AWARD", "center": "External", "@type": ["Award", "Item"], "name": "external-award", "uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "description": "Funding source is from outside 4DN.", "center_title": "External", "@id": "/awards/external-award/", "status": "current", "project": "External", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "fabeecc9ce10a05d019177ef7bb66998", "status": "released", "aliases": ["4dn-dcic-lab:SRR5339812_2_fq"], "dbxrefs": ["SRA:SRR5339812"], "filename": "SRR5339812_2.fastq.gz", "accession": "4DNFIMKRJZFP", "file_size": 10658359797, "file_type": "reads", "instrument": "Illumina HiSeq 2000", "paired_end": "2", "file_format": {"display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "read_length": 49, "date_created": "2019-08-12T14:49:57.406524+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2020-04-07T03:38:46.113050+00:00"}, "related_files": [{"file": {"@id": "/files-fastq/4DNFIWI3OZ2S/", "uuid": "d1346f37-c64b-4519-a852-4776ca074507", "display_title": "4DNFIWI3OZ2S.fastq.gz", "status": "released", "accession": "4DNFIWI3OZ2S", "@type": ["FileFastq", "File", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "relationship_type": "paired with"}], "content_md5sum": "c6561a520dbc4c1325d88bc72a0002de", "public_release": "2019-12-01", "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIMKRJZFP/fastqc_report.html", "Total Sequences": 255425149, "overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/4a4f63d9-4809-4c01-9ed4-eb9469a54f7f/", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "status": "released", "display_title": "QualityMetricFastqc from 2019-08-22", "uuid": "4a4f63d9-4809-4c01-9ed4-eb9469a54f7f", "Sequence length": "48", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "schema_version": "2", "file_first_line": "@HWI-D00175:372:C7ML5ANXX:5:1101:1194:1998", "project_release": "2019-12-01", "file_classification": "raw file", "@id": "/files-fastq/4DNFIMKRJZFP/", "@type": ["FileFastq", "File", "Item"], "uuid": "8724f3d8-b653-42f8-9db4-a976d95a5cc3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNFIMKRJZFP.fastq.gz", "external_references": [{"ref": "SRA:SRR5339812", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5339812"}], "experiments": [{"accession": "4DNEXYY2LOHJ", "uuid": "40ccbc73-3d3d-4b8b-abb2-272a01cb8092", "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"], "biosample": {"modifications_summary": "None", "@id": "/biosamples/4DNBSMW9D9G9/", "biosource_summary": "46C with Sox1-GFP", "uuid": "910d420f-1977-4507-b476-601535b60181", "status": "released", "accession": "4DNBSMW9D9G9", "display_title": "4DNBSMW9D9G9", "@type": ["Biosample", "Item"], "treatments_summary": "None", "biosource": [{"@type": ["Biosource", "Item"], "@id": "/biosources/4DNSRNTW8KVA/", "status": "released", "display_title": "46C with Sox1-GFP - 4DNSRNTW8KVA", "cell_line_tier": "Unclassified", "override_biosource_name": "46C with Sox1-GFP", "uuid": "15180a95-b2ca-4be7-99b1-7a9f7b2620aa", "biosource_type": "stem cell derived cell line", "modifications": [{"modification_type": "Stable Transfection", "@type": ["Modification", "Item"], "genomic_change": "replacement", "status": "released", "uuid": "acd9be42-59e6-4c5b-983d-1a61208cb29d", "@id": "/modifications/acd9be42-59e6-4c5b-983d-1a61208cb29d/", "display_title": "Stable Transfection replacement for Sox1 mouse gene", "target_of_mod": [{"organism_name": "mouse", "@type": ["BioFeature", "Item"], "display_title": "Sox1 mouse gene", "status": "released", "@id": "/bio-features/6d5fb946-7a9f-4c67-9cd3-0037862afdc6/", "uuid": "6d5fb946-7a9f-4c67-9cd3-0037862afdc6", "relevant_genes": [{"@id": "/genes/20664/", "uuid": "017608e0-9f01-4173-ac83-d2a3d99e28bb", "status": "released", "@type": ["Gene", "Item"], "display_title": "Sox1", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "feature_type": {"uuid": "0231da78-1adc-4b8a-89b9-4f91908412a3", "@id": "/ontology-terms/SO:0000704/", "@type": ["OntologyTerm", "Item"], "status": "released", "display_title": "gene", "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": {"@id": "/organisms/10090/", "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "scientific_name": "Mus musculus", "name": "mouse", "display_title": "M. musculus", "@type": ["Organism", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"display_title": "4DNINES2PTTN", "uuid": "fb69d05b-0e11-4d5e-bace-a9767f9c9e81", "@id": "/individuals-mouse/4DNINES2PTTN/", "@type": ["IndividualMouse", "Individual", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"@type": ["OntologyTerm", "Item"], "status": "released", "display_title": "stem cell", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "term_id": "CL:0000034", "term_name": "stem cell", "@id": "/ontology-terms/CL:0000034/", "preferred_name": "stem cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "cell_line": {"preferred_name": "46C", "term_name": "46C", "@id": "/ontology-terms/EFO:0005484/", "status": "released", "display_title": "46C", "uuid": "1dd66cb6-7900-405f-a7ea-0f88966ca969", "@type": ["OntologyTerm", "Item"], "term_id": "EFO:0005484", "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", "@id": "/biosample-cell-cultures/345928f0-d02d-4dab-a794-21e35540ed82/", "in_vitro_differentiated": "Yes", "uuid": "345928f0-d02d-4dab-a794-21e35540ed82", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "digestion_enzyme": {"uuid": "356a57a1-1f1d-463d-a972-27742f79a6a5", "name": "DpnII", "display_title": "DpnII", "@type": ["Enzyme", "Item"], "@id": "/enzymes/DpnII/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_sets": [{"@id": "/experiment-set-replicates/4DNESJ9SIAV5/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "experimentset_type": "replicate", "display_title": "4DNESJ9SIAV5", "uuid": "458e5476-8946-4820-af50-95c25fff73b2", "status": "released", "accession": "4DNESJ9SIAV5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_type": {"status": "released", "@type": ["ExperimentType", "Item"], "title": "in situ Hi-C", "display_title": "in situ Hi-C", "uuid": "a2920a38-cdba-4ff0-b4f0-c6bb53257747", "@id": "/experiment-types/in-situ-hi-c/", "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": "4DNFIMKRJZFP", "href": "/files-fastq/4DNFIMKRJZFP/@@download/4DNFIMKRJZFP.fastq.gz", "upload_key": "8724f3d8-b653-42f8-9db4-a976d95a5cc3/4DNFIMKRJZFP.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/8724f3d8-b653-42f8-9db4-a976d95a5cc3/4DNFIMKRJZFP.fastq.gz", "tsv_notes": "", "workflow_run_inputs": [{"display_title": "fastqc v1 run 2019-08-22 00:28:21.694431", "uuid": "04030658-aa1d-49d7-a660-86d282e0c4d5", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "@id": "/workflow-runs-awsem/04030658-aa1d-49d7-a660-86d282e0c4d5/", "status": "released", "workflow": {"uuid": "2324ad76-ff37-4157-8bcc-3ce72b7dace9", "title": "FastQC v1", "display_title": "FastQC v1 - 4DNWFAW5VTA5", "@id": "/workflows/4DNWFAW5VTA5/", "@type": ["Workflow", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "output_files": [{"workflow_argument_name": "report_zip", "value_qc": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIMKRJZFP/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/4a4f63d9-4809-4c01-9ed4-eb9469a54f7f/", "status": "released", "uuid": "4a4f63d9-4809-4c01-9ed4-eb9469a54f7f", "display_title": "QualityMetricFastqc from 2019-08-22", "overall_quality_status": "PASS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "input_files": [{"workflow_argument_name": "input_fastq", "value": {"@id": "/files-fastq/4DNFIMKRJZFP/", "accession": "4DNFIMKRJZFP", "@type": ["FileFastq", "File", "Item"], "filename": "SRR5339812_2.fastq.gz", "display_title": "4DNFIMKRJZFP.fastq.gz", "status": "released", "uuid": "8724f3d8-b653-42f8-9db4-a976d95a5cc3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "md5 0.2.6 run 2019-08-21 23:12:31.135206", "uuid": "bc25fdcd-b74a-488b-ba43-78c0494531c8", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "@id": "/workflow-runs-awsem/bc25fdcd-b74a-488b-ba43-78c0494531c8/", "status": "released", "workflow": {"uuid": "c77a117b-9a58-477e-aaa5-291a109a99f6", "title": "md5 0.2.6", "display_title": "md5 0.2.6 - 4DNWF2HFF82B", "@id": "/workflows/4DNWF2HFF82B/", "@type": ["Workflow", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "output_files": [{"workflow_argument_name": "report"}], "input_files": [{"workflow_argument_name": "input_file", "value": {"@id": "/files-fastq/4DNFIMKRJZFP/", "accession": "4DNFIMKRJZFP", "@type": ["FileFastq", "File", "Item"], "filename": "SRR5339812_2.fastq.gz", "display_title": "4DNFIMKRJZFP.fastq.gz", "status": "released", "uuid": "8724f3d8-b653-42f8-9db4-a976d95a5cc3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "display_title": "fastq", "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 03:06:27.232465", "uuid": "fcbc6bdf-575f-46b5-ab4c-e53cb6dc7939", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "@id": "/workflow-runs-awsem/fcbc6bdf-575f-46b5-ab4c-e53cb6dc7939/", "status": "released", "workflow": {"uuid": "3feedadc-50f9-4bb4-919b-09a8b731d0cc", "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/", "@type": ["Workflow", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "output_files": [{"workflow_argument_name": "out_bam", "value": {"accession": "4DNFIPYNXBFQ", "@type": ["FileProcessed", "File", "Item"], "uuid": "54503b08-9cdb-486c-be8e-62f7bfe3cc7e", "display_title": "4DNFIPYNXBFQ.bam", "@id": "/files-processed/4DNFIPYNXBFQ/", "status": "released", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "display_title": "bam", "status": "released", "file_format": "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": {"@id": "/files-reference/4DNFI823LSI8/", "accession": "4DNFI823LSI8", "@type": ["FileReference", "File", "Item"], "filename": "mm10.bwaIndex.tgz", "display_title": "4DNFI823LSI8.bwaIndex.tgz", "status": "released", "uuid": "4a6d10ee-2edb-4402-a98f-0edb1d58f5e1", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "bwaIndex", "status": "released", "uuid": "d13d06cf-218e-4f61-55f0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bwaIndex/", "display_title": "bwaIndex", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"workflow_argument_name": "fastq1", "value": {"@id": "/files-fastq/4DNFIWI3OZ2S/", "accession": "4DNFIWI3OZ2S", "@type": ["FileFastq", "File", "Item"], "filename": "SRR5339812_1.fastq.gz", "display_title": "4DNFIWI3OZ2S.fastq.gz", "status": "released", "uuid": "d1346f37-c64b-4519-a852-4776ca074507", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"workflow_argument_name": "fastq2", "value": {"@id": "/files-fastq/4DNFIMKRJZFP/", "accession": "4DNFIMKRJZFP", "@type": ["FileFastq", "File", "Item"], "filename": "SRR5339812_2.fastq.gz", "display_title": "4DNFIMKRJZFP.fastq.gz", "status": "released", "uuid": "8724f3d8-b653-42f8-9db4-a976d95a5cc3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "display_title": "fastq", "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 03:33:35.089503", "uuid": "4f026bd9-6308-46f1-8cea-80f8f216e750", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "@id": "/workflow-runs-awsem/4f026bd9-6308-46f1-8cea-80f8f216e750/", "status": "released", "workflow": {"uuid": "93a1a931-d55d-4623-adfb-0fa735daf6ae", "title": "Getting first line of fastq file", "display_title": "Getting first line of fastq file - 4DNWFASTQFO1", "@id": "/workflows/4DNWFASTQFO1/", "@type": ["Workflow", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "output_files": [{"workflow_argument_name": "first_line"}], "input_files": [{"workflow_argument_name": "fastq", "value": {"@id": "/files-fastq/4DNFIMKRJZFP/", "accession": "4DNFIMKRJZFP", "@type": ["FileFastq", "File", "Item"], "filename": "SRR5339812_2.fastq.gz", "display_title": "4DNFIMKRJZFP.fastq.gz", "status": "released", "uuid": "8724f3d8-b653-42f8-9db4-a976d95a5cc3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "fastq", "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "display_title": "fastq", "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": []}