{"lab": {"title": "Benoit Bruneau, UCSF", "display_title": "Benoit Bruneau, UCSF", "@id": "/labs/benoit-bruneau-lab/", "correspondence": [{"contact_email": "YmVub2l0LmJydW5lYXVAZ2xhZHN0b25lLnVjc2YuZWR1", "@id": "/users/c015dffd-4ca1-4070-905f-8a04b3754b2b/", "display_title": "Benoit Bruneau"}], "status": "current", "uuid": "4dfac8f5-a868-4b29-9c11-a0932130e121", "@type": ["Lab", "Item"], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.4dfac8f5-a868-4b29-9c11-a0932130e121"]}}, "award": {"status": "current", "@id": "/awards/external-award/", "uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "display_title": "EXTERNAL AWARD", "@type": ["Award", "Item"], "center_title": "External", "description": "Funding source is from outside 4DN.", "name": "external-award", "project": "External", "center": "External", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "3515ea6e705b259cbc03a8a0f6d79e96", "status": "released", "aliases": ["4dn-dcic-lab:SRR5633694_2_fq"], "dbxrefs": ["SRA:SRR5633694"], "filename": "SRR5633694_2.fastq.gz", "accession": "4DNFIW795KTK", "file_size": 18822200499, "file_type": "reads", "instrument": "Illumina HiSeq 4000", "paired_end": "2", "file_format": {"@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "display_title": "fastq", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "read_length": 75, "date_created": "2018-11-07T21:12:11.892324+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2020-04-08T06:01:25.190165+00:00"}, "related_files": [{"file": {"@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIFQPFVJV.fastq.gz", "@id": "/files-fastq/4DNFIFQPFVJV/", "uuid": "2d4f8c04-0431-4987-aa56-c05a6bec7aab", "status": "released", "accession": "4DNFIFQPFVJV", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "relationship_type": "paired with"}], "content_md5sum": "2e05b4c5ce25f43d6f63f17bbe123f4a", "public_release": "2018-12-06", "quality_metric": {"Sequence length": "100", "@id": "/quality-metrics-fastqc/a1f13c45-0860-4074-9246-3da96dc7767f/", "uuid": "a1f13c45-0860-4074-9246-3da96dc7767f", "overall_quality_status": "PASS", "status": "released", "display_title": "QualityMetricFastqc from 2018-11-20", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIW795KTK/fastqc_report.html", "Total Sequences": 357800221, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "schema_version": "2", "file_first_line": "@1", "project_release": "2018-12-06", "file_classification": "raw file", "@id": "/files-fastq/4DNFIW795KTK/", "@type": ["FileFastq", "File", "Item"], "uuid": "9d8bd06f-024f-4ae3-8954-a427b9348028", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNFIW795KTK.fastq.gz", "external_references": [{"ref": "SRA:SRR5633694", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5633694"}], "experiments": [{"@id": "/experiments-hi-c/4DNEXT3IN9TT/", "status": "released", "display_title": "Dilution Hi-C on ES-E14TG2a with CTCF-AID with HindIII - 4DNEXT3IN9TT", "uuid": "fefc9c46-87d2-4e50-a6c6-85b078a74a67", "accession": "4DNEXT3IN9TT", "@type": ["ExperimentHiC", "Experiment", "Item"], "biosample": {"biosource_summary": "ES-E14TG2a with CTCF-AID", "modifications_summary": "None", "treatments_summary": "None", "@type": ["Biosample", "Item"], "status": "released", "@id": "/biosamples/4DNBS51BW1AU/", "uuid": "f14888c3-9abc-4ef0-8a31-7291480dddbe", "display_title": "4DNBS51BW1AU", "accession": "4DNBS51BW1AU", "biosource": [{"cell_line_tier": "Unclassified", "biosource_type": "stem cell derived cell line", "display_title": "ES-E14TG2a with CTCF-AID - 4DNSRLMKMT14", "@type": ["Biosource", "Item"], "override_biosource_name": "ES-E14TG2a with CTCF-AID", "status": "released", "@id": "/biosources/4DNSRLMKMT14/", "uuid": "9fd3c189-7169-4336-bfd1-545c3b53ca44", "organism": {"name": "mouse", "status": "released", "display_title": "M. musculus", "@id": "/organisms/10090/", "@type": ["Organism", "Item"], "scientific_name": "Mus musculus", "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/CL:0000034/", "status": "released", "term_name": "stem cell", "display_title": "stem cell", "term_id": "CL:0000034", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "preferred_name": "stem cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "modifications": [{"modification_type": "Crispr", "genomic_change": "insertion", "@id": "/modifications/4c0507ac-3639-4afa-a0d7-f0c969ac0f09/", "display_title": "CTCF tagged with AID-eGFP", "uuid": "4c0507ac-3639-4afa-a0d7-f0c969ac0f09", "status": "released", "@type": ["Modification", "Item"], "override_modification_name": "CTCF tagged with AID-eGFP", "target_of_mod": [{"uuid": "d9c1b491-a1d8-4b93-9d33-fce884c4257e", "display_title": "Ctcf mouse gene", "@type": ["BioFeature", "Item"], "organism_name": "mouse", "status": "released", "@id": "/bio-features/d9c1b491-a1d8-4b93-9d33-fce884c4257e/", "relevant_genes": [{"@id": "/genes/13018/", "uuid": "a8dfeefd-d3bc-45cb-be3b-65d7bb4de27e", "@type": ["Gene", "Item"], "status": "released", "display_title": "Ctcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "feature_type": {"status": "released", "@id": "/ontology-terms/SO:0000704/", "uuid": "0231da78-1adc-4b8a-89b9-4f91908412a3", "display_title": "gene", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"modification_type": "Stable Transfection", "genomic_change": "insertion", "@id": "/modifications/4ec97b91-8bec-44bb-a43c-655f5d4a246e/", "display_title": "Tir1 random insertion", "uuid": "4ec97b91-8bec-44bb-a43c-655f5d4a246e", "status": "released", "@type": ["Modification", "Item"], "override_modification_name": "Tir1 random insertion", "target_of_mod": [{"uuid": "9a6e3474-a523-4d87-8903-65031b2cf024", "display_title": "Tir1 (Japanese rice)", "@type": ["BioFeature", "Item"], "organism_name": "Japanese rice", "preferred_label": "Tir1", "status": "released", "@id": "/bio-features/9a6e3474-a523-4d87-8903-65031b2cf024/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "feature_type": {"status": "released", "@id": "/ontology-terms/SO:0000104/", "uuid": "91f427e6-5246-4992-8123-b4f8fa9eef01", "display_title": "protein", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "individual": {"status": "released", "@id": "/individuals-mouse/4DNINOXRXEQP/", "display_title": "4DNINOXRXEQP", "uuid": "1b2fa35a-6173-431f-b2e2-db2e18017870", "@type": ["IndividualMouse", "Individual", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "cell_line": {"status": "released", "preferred_name": "ES-E14TG2a", "uuid": "2262fd9b-3185-4c65-8ad5-bfe65e986954", "term_name": "ES-E14TG2a", "@id": "/ontology-terms/EFO:0006275/", "term_id": "EFO:0006275", "@type": ["OntologyTerm", "Item"], "display_title": "ES-E14TG2a", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_type": {"status": "released", "uuid": "832b7989-69ab-4bb6-97b9-195d5dd965ea", "@type": ["ExperimentType", "Item"], "title": "Dilution Hi-C", "@id": "/experiment-types/dilution-hi-c/", "display_title": "Dilution Hi-C", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_sets": [{"@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "@id": "/experiment-set-replicates/4DNESIYG3BXA/", "status": "released", "uuid": "85342001-93f5-419e-884a-267950bc87fa", "experimentset_type": "replicate", "display_title": "4DNESIYG3BXA", "accession": "4DNESIYG3BXA", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "digestion_enzyme": {"@id": "/enzymes/HindIII/", "uuid": "2ace2f00-c913-4bac-a6ef-0b316bc2108e", "status": "released", "display_title": "HindIII", "name": "HindIII", "@type": ["Enzyme", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2019-05-14T20:01:20.980309+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "file_type_detailed": "reads (fastq)", "track_and_facet_info": {"experimental_lab": "Benoit Bruneau, UCSF", "experiment_type": "Dilution Hi-C", "experiment_bucket": "raw file", "assay_info": "HindIII", "dataset": "Hi-C on CTCF-AID tagged mESCs", "condition": "CTCF-depletion by auxin treatment followed by 24h wash-off", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "ES-E14TG2a with CTCF-AID", "lab_name": "Benoit Bruneau, UCSF"}, "title": "4DNFIW795KTK", "href": "/files-fastq/4DNFIW795KTK/@@download/4DNFIW795KTK.fastq.gz", "upload_key": "9d8bd06f-024f-4ae3-8954-a427b9348028/4DNFIW795KTK.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/9d8bd06f-024f-4ae3-8954-a427b9348028/4DNFIW795KTK.fastq.gz", "tsv_notes": "", "workflow_run_inputs": [{"display_title": "md5 0.2.6 run 2018-11-19 22:16:57.534510", "uuid": "7c68b1fa-5cd0-4608-b7ab-af9e39bdbed5", "@id": "/workflow-runs-awsem/7c68b1fa-5cd0-4608-b7ab-af9e39bdbed5/", "status": "released", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "output_files": [{"workflow_argument_name": "report"}], "input_files": [{"workflow_argument_name": "input_file", "value": {"filename": "SRR5633694_2.fastq.gz", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIW795KTK", "display_title": "4DNFIW795KTK.fastq.gz", "uuid": "9d8bd06f-024f-4ae3-8954-a427b9348028", "@id": "/files-fastq/4DNFIW795KTK/", "status": "released", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "display_title": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"status": "released", "@type": ["Workflow", "Item"], "display_title": "md5 0.2.6 - 4DNWF2HFF82B", "title": "md5 0.2.6", "uuid": "c77a117b-9a58-477e-aaa5-291a109a99f6", "@id": "/workflows/4DNWF2HFF82B/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "fastqc v1 run 2018-11-19 22:17:01.362275", "uuid": "c713a86b-d81b-4e23-9c46-89f47cd3808d", "@id": "/workflow-runs-awsem/c713a86b-d81b-4e23-9c46-89f47cd3808d/", "status": "released", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "output_files": [{"workflow_argument_name": "report_zip", "value_qc": {"@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "a1f13c45-0860-4074-9246-3da96dc7767f", "display_title": "QualityMetricFastqc from 2018-11-20", "@id": "/quality-metrics-fastqc/a1f13c45-0860-4074-9246-3da96dc7767f/", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIW795KTK/fastqc_report.html", "overall_quality_status": "PASS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "input_files": [{"workflow_argument_name": "input_fastq", "value": {"filename": "SRR5633694_2.fastq.gz", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIW795KTK", "display_title": "4DNFIW795KTK.fastq.gz", "uuid": "9d8bd06f-024f-4ae3-8954-a427b9348028", "@id": "/files-fastq/4DNFIW795KTK/", "status": "released", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "display_title": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"status": "released", "@type": ["Workflow", "Item"], "display_title": "FastQC v1 - 4DNWFAW5VTA5", "title": "FastQC v1", "uuid": "2324ad76-ff37-4157-8bcc-3ce72b7dace9", "@id": "/workflows/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 2018-11-30 05:30:59.690452", "uuid": "ab48587f-ef0d-4f7e-97b0-8149f3587d1f", "@id": "/workflow-runs-awsem/ab48587f-ef0d-4f7e-97b0-8149f3587d1f/", "status": "released", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "output_files": [{"workflow_argument_name": "out_bam", "value": {"status": "released", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFIXUEMEW9", "uuid": "f3c3c118-c1ba-4031-9545-dec3e2b0846e", "@id": "/files-processed/4DNFIXUEMEW9/", "display_title": "4DNFIXUEMEW9.bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bam", "file_format": "bam", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@id": "/file-formats/bam/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "input_files": [{"workflow_argument_name": "bwa_index", "value": {"filename": "mm10.bwaIndex.tgz", "@type": ["FileReference", "File", "Item"], "accession": "4DNFI823LSI8", "display_title": "4DNFI823LSI8.bwaIndex.tgz", "uuid": "4a6d10ee-2edb-4402-a98f-0edb1d58f5e1", "@id": "/files-reference/4DNFI823LSI8/", "status": "released", "file_format": {"uuid": "d13d06cf-218e-4f61-55f0-91f226248b2c", "@id": "/file-formats/bwaIndex/", "display_title": "bwaIndex", "status": "released", "@type": ["FileFormat", "Item"], "file_format": "bwaIndex", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "fastq1", "value": {"filename": "SRR5633694_1.fastq.gz", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIFQPFVJV", "display_title": "4DNFIFQPFVJV.fastq.gz", "uuid": "2d4f8c04-0431-4987-aa56-c05a6bec7aab", "@id": "/files-fastq/4DNFIFQPFVJV/", "status": "released", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "display_title": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "fastq2", "value": {"filename": "SRR5633694_2.fastq.gz", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIW795KTK", "display_title": "4DNFIW795KTK.fastq.gz", "uuid": "9d8bd06f-024f-4ae3-8954-a427b9348028", "@id": "/files-fastq/4DNFIW795KTK/", "status": "released", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "display_title": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"status": "released", "@type": ["Workflow", "Item"], "display_title": "Alignment for Hi-C using bwa-mem 0.2.6 - 4DNWF84NFOQP", "title": "Alignment for Hi-C using bwa-mem 0.2.6", "uuid": "3feedadc-50f9-4bb4-919b-09a8b731d0cc", "@id": "/workflows/4DNWF84NFOQP/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "fastq-first-line v2 run 2020-04-08 05:56:15.095944", "uuid": "3d8f6332-fcc0-4f27-a7c3-a48776c747ba", "@id": "/workflow-runs-awsem/3d8f6332-fcc0-4f27-a7c3-a48776c747ba/", "status": "released", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "output_files": [{"workflow_argument_name": "first_line"}], "input_files": [{"workflow_argument_name": "fastq", "value": {"filename": "SRR5633694_2.fastq.gz", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIW795KTK", "display_title": "4DNFIW795KTK.fastq.gz", "uuid": "9d8bd06f-024f-4ae3-8954-a427b9348028", "@id": "/files-fastq/4DNFIW795KTK/", "status": "released", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "display_title": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"status": "released", "@type": ["Workflow", "Item"], "display_title": "Getting first line of fastq file - 4DNWFASTQFO1", "title": "Getting first line of fastq file", "uuid": "93a1a931-d55d-4623-adfb-0fa735daf6ae", "@id": "/workflows/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": []}