{"lab": {"display_title": "Job Dekker, UMMS", "@id": "/labs/job-dekker-lab/", "title": "Job Dekker, UMMS", "status": "current", "correspondence": [{"contact_email": "am9iLmRla2tlckB1bWFzc21lZC5lZHU=", "@id": "/users/83b5073a-069b-4162-9b30-6f42d5551e34/", "display_title": "Job Dekker"}], "@type": ["Lab", "Item"], "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}, "award": {"uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "@type": ["Award", "Item"], "status": "current", "project": "External", "description": "Funding source is from outside 4DN.", "center_title": "External", "name": "external-award", "center": "External", "display_title": "EXTERNAL AWARD", "@id": "/awards/external-award/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "d7b31774999232f207ccfcae620f9a13", "status": "released", "aliases": ["4dn-dcic-lab:SRR5939681_2_fq"], "dbxrefs": ["SRA:SRR5939681"], "filename": "SRR5939681_2.fastq.gz", "accession": "4DNFIXV4QI5Z", "file_size": 11274157910, "file_type": "reads", "instrument": "Illumina HiSeq 4000", "paired_end": "2", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "read_length": 50, "date_created": "2018-10-30T17:23:17.846986+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2020-04-08T06:21:04.606857+00:00"}, "related_files": [{"file": {"status": "released", "accession": "4DNFIVCCTJCI", "display_title": "4DNFIVCCTJCI.fastq.gz", "uuid": "53ccd95f-03eb-4c56-8547-52a423f2da28", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIVCCTJCI/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "relationship_type": "paired with"}], "content_md5sum": "55728066ee33dbad2e9b4a0a438f24b2", "public_release": "2019-10-11", "quality_metric": {"@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "display_title": "QualityMetricFastqc from 2018-11-16", "Sequence length": "50", "overall_quality_status": "PASS", "Total Sequences": 386311409, "status": "released", "@id": "/quality-metrics-fastqc/cba468aa-5329-4b21-8361-cfc461a3f490/", "uuid": "cba468aa-5329-4b21-8361-cfc461a3f490", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIXV4QI5Z/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "schema_version": "2", "file_first_line": "@1", "project_release": "2019-10-11", "file_classification": "raw file", "@id": "/files-fastq/4DNFIXV4QI5Z/", "@type": ["FileFastq", "File", "Item"], "uuid": "dea8d5cd-60fe-436f-bbb0-d65d6e217e1c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNFIXV4QI5Z.fastq.gz", "external_references": [{"ref": "SRA:SRR5939681", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5939681"}], "experiments": [{"display_title": "Dilution Hi-C on DT40 with random integration of GFP and AID-tagged CAP-H2 gene, NCAPH2 disruption, random integration of X. laevis Cdk1, CDK1 disruption with HindIII - 4DNEXQ4RGG3Q", "accession": "4DNEXQ4RGG3Q", "@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "e41c51dd-5a1d-4d33-9518-aabb5de93ccd", "@id": "/experiments-hi-c/4DNEXQ4RGG3Q/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "experiment_type": {"@type": ["ExperimentType", "Item"], "@id": "/experiment-types/dilution-hi-c/", "uuid": "832b7989-69ab-4bb6-97b9-195d5dd965ea", "status": "released", "title": "Dilution Hi-C", "display_title": "Dilution Hi-C", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "biosample": {"biosource_summary": "DT40 with random integration of GFP and AID-tagged CAP-H2 gene, NCAPH2 disruption, random integration of X. laevis Cdk1, CDK1 disruption", "display_title": "4DNBSJLMGA2S", "@type": ["Biosample", "Item"], "treatments_summary": "1NM-PP1 treatment (2.0 \u03bcM, 13.0h) and Auxin treatment (125 \u03bcM)", "@id": "/biosamples/4DNBSJLMGA2S/", "status": "released", "uuid": "89515861-74ea-466c-8445-28aa8620d924", "accession": "4DNBSJLMGA2S", "modifications_summary": "None", "biosource": [{"biosource_type": "immortalized cell line", "uuid": "0e212fbb-0895-4cbd-b29e-4baead329adc", "status": "released", "@id": "/biosources/4DNSRHKEBVUK/", "@type": ["Biosource", "Item"], "display_title": "DT40 with random integration of GFP and AID-tagged CAP-H2 gene, NCAPH2 disruption, random integration of X. laevis Cdk1, CDK1 disruption - 4DNSRHKEBVUK", "cell_line_tier": "Unclassified", "tissue": {"@type": ["OntologyTerm", "Item"], "status": "released", "display_title": "bursa of Fabricius", "term_id": "UBERON:0003903", "@id": "/ontology-terms/UBERON:0003903/", "preferred_name": "bursa of Fabricius", "uuid": "1bfd1088-3311-4711-8c41-83dbed3db972", "term_name": "bursa of Fabricius", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "modifications": [{"status": "released", "@id": "/modifications/5384182d-cedf-45c8-a97b-35262bfc7615/", "uuid": "5384182d-cedf-45c8-a97b-35262bfc7615", "display_title": "random integration of GFP and AID-tagged CAP-H2 gene", "override_modification_name": "random integration of GFP and AID-tagged CAP-H2 gene", "genomic_change": "insertion", "@type": ["Modification", "Item"], "modification_type": "Stable Transfection", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "@id": "/modifications/0bd91d0a-3494-49e1-b444-5e1c5c03172b/", "uuid": "0bd91d0a-3494-49e1-b444-5e1c5c03172b", "display_title": "Crispr disruption for NCAPH2 chicken gene", "genomic_change": "disruption", "@type": ["Modification", "Item"], "modification_type": "Crispr", "target_of_mod": [{"organism_name": "chicken", "display_title": "NCAPH2 chicken gene", "uuid": "421e9d46-1f26-4f5e-a0f4-4328099af885", "status": "released", "@id": "/bio-features/421e9d46-1f26-4f5e-a0f4-4328099af885/", "@type": ["BioFeature", "Item"], "feature_type": {"display_title": "gene", "status": "released", "uuid": "0231da78-1adc-4b8a-89b9-4f91908412a3", "@id": "/ontology-terms/SO:0000704/", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "relevant_genes": [{"uuid": "d699c872-e111-4646-9741-6215ea152152", "@type": ["Gene", "Item"], "display_title": "NCAPH2", "@id": "/genes/426276/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "@id": "/modifications/4dca1ddb-ab74-44f5-ac84-738b0198886d/", "uuid": "4dca1ddb-ab74-44f5-ac84-738b0198886d", "display_title": "random integration of X. laevis Cdk1", "override_modification_name": "random integration of X. laevis Cdk1", "genomic_change": "insertion", "@type": ["Modification", "Item"], "modification_type": "Stable Transfection", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "@id": "/modifications/fb27fdf6-4199-4179-8bb0-6101b1404aee/", "uuid": "fb27fdf6-4199-4179-8bb0-6101b1404aee", "display_title": "Crispr disruption for CDK1 chicken gene", "genomic_change": "disruption", "@type": ["Modification", "Item"], "modification_type": "Crispr", "target_of_mod": [{"organism_name": "chicken", "display_title": "CDK1 chicken gene", "uuid": "03ca1ef3-0276-46ce-b277-13c123c9e520", "status": "released", "@id": "/bio-features/03ca1ef3-0276-46ce-b277-13c123c9e520/", "@type": ["BioFeature", "Item"], "feature_type": {"display_title": "gene", "status": "released", "uuid": "0231da78-1adc-4b8a-89b9-4f91908412a3", "@id": "/ontology-terms/SO:0000704/", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "relevant_genes": [{"uuid": "ecf839a7-e4fb-4703-a47b-b36d8562ea2c", "@type": ["Gene", "Item"], "display_title": "CDK1", "@id": "/genes/396252/", "status": "released", "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": {"uuid": "fed8c206-762f-497f-821b-1c8ff7900bd2", "name": "chicken", "status": "released", "scientific_name": "Gallus gallus", "@type": ["Organism", "Item"], "display_title": "G. gallus", "@id": "/organisms/9031/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "cell_line": {"@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/EFO:0006274/", "term_name": "DT40", "term_id": "EFO:0006274", "display_title": "DT40", "preferred_name": "DT40", "uuid": "fd057734-0765-4007-b7eb-d71ac7cbef65", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"uuid": "836856fd-a0f7-4daf-afb2-4a098df8e8fc", "@id": "/individuals-chicken/4DNINYWTTO3D/", "@type": ["IndividualChicken", "Individual", "Item"], "display_title": "4DNINYWTTO3D", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_sets": [{"uuid": "7d9bb2ba-acfe-4f68-ba09-d8a111461897", "accession": "4DNES3CEBN3H", "experimentset_type": "replicate", "display_title": "4DNES3CEBN3H", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "status": "released", "@id": "/experiment-set-replicates/4DNES3CEBN3H/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "digestion_enzyme": {"status": "released", "name": "HindIII", "uuid": "2ace2f00-c913-4bac-a6ef-0b316bc2108e", "@id": "/enzymes/HindIII/", "display_title": "HindIII", "@type": ["Enzyme", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2019-10-11T20:54:43.702381+00:00"}}], "file_type_detailed": "reads (fastq)", "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Dilution Hi-C", "experiment_bucket": "raw file", "assay_info": "HindIII", "dataset": "HiC on sync. CAPH2-AID chicken cells", "condition": "prophase (10m), CAPH2-", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "DT40 with random integration of GFP and AID-tagged CAP-H2 gene, NCAPH2 disruption, random integration of X. laevis Cdk1, CDK1 disruption", "lab_name": "Job Dekker, UMMS"}, "title": "4DNFIXV4QI5Z", "href": "/files-fastq/4DNFIXV4QI5Z/@@download/4DNFIXV4QI5Z.fastq.gz", "upload_key": "dea8d5cd-60fe-436f-bbb0-d65d6e217e1c/4DNFIXV4QI5Z.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/dea8d5cd-60fe-436f-bbb0-d65d6e217e1c/4DNFIXV4QI5Z.fastq.gz", "tsv_notes": "", "workflow_run_inputs": [{"@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "@id": "/workflow-runs-awsem/7a7952dc-6756-4ad3-9320-2e64b24f1667/", "status": "released", "uuid": "7a7952dc-6756-4ad3-9320-2e64b24f1667", "display_title": "md5 0.2.6 run 2018-11-15 20:57:40.426002", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "output_files": [{"workflow_argument_name": "report"}], "input_files": [{"workflow_argument_name": "input_file", "value": {"status": "released", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIXV4QI5Z.fastq.gz", "uuid": "dea8d5cd-60fe-436f-bbb0-d65d6e217e1c", "accession": "4DNFIXV4QI5Z", "@id": "/files-fastq/4DNFIXV4QI5Z/", "filename": "SRR5939681_2.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "workflow": {"display_title": "md5 0.2.6 - 4DNWF2HFF82B", "title": "md5 0.2.6", "@type": ["Workflow", "Item"], "@id": "/workflows/4DNWF2HFF82B/", "status": "released", "uuid": "c77a117b-9a58-477e-aaa5-291a109a99f6", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "@id": "/workflow-runs-awsem/63c42a1f-bb0a-4333-b5e5-34e872d8b2f0/", "status": "released", "uuid": "63c42a1f-bb0a-4333-b5e5-34e872d8b2f0", "display_title": "fastqc v1 run 2018-11-15 20:57:43.695495", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "output_files": [{"workflow_argument_name": "report_zip", "value_qc": {"@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "cba468aa-5329-4b21-8361-cfc461a3f490", "status": "released", "display_title": "QualityMetricFastqc from 2018-11-16", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIXV4QI5Z/fastqc_report.html", "@id": "/quality-metrics-fastqc/cba468aa-5329-4b21-8361-cfc461a3f490/", "overall_quality_status": "PASS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "input_files": [{"workflow_argument_name": "input_fastq", "value": {"status": "released", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIXV4QI5Z.fastq.gz", "uuid": "dea8d5cd-60fe-436f-bbb0-d65d6e217e1c", "accession": "4DNFIXV4QI5Z", "@id": "/files-fastq/4DNFIXV4QI5Z/", "filename": "SRR5939681_2.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "workflow": {"display_title": "FastQC v1 - 4DNWFAW5VTA5", "title": "FastQC v1", "@type": ["Workflow", "Item"], "@id": "/workflows/4DNWFAW5VTA5/", "status": "released", "uuid": "2324ad76-ff37-4157-8bcc-3ce72b7dace9", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "@id": "/workflow-runs-awsem/39a54d38-ecfb-47bf-849a-cefa383ccb9f/", "status": "released", "uuid": "39a54d38-ecfb-47bf-849a-cefa383ccb9f", "display_title": "bwa-mem 0.2.6 run 2018-12-04 06:43:37.124285", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "output_files": [{"workflow_argument_name": "out_bam", "value": {"uuid": "ced4d300-3a84-4d1a-a50b-e5b16fbdf950", "status": "released", "accession": "4DNFIQMMQ6ST", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIQMMQ6ST/", "display_title": "4DNFIQMMQ6ST.bam", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "@id": "/file-formats/bam/", "file_format": "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": {"status": "released", "@type": ["FileReference", "File", "Item"], "display_title": "4DNFIVGRYVQF.bwaIndex.tgz", "uuid": "0e2ac53a-a7e4-4681-b7e9-c1012715b46e", "accession": "4DNFIVGRYVQF", "@id": "/files-reference/4DNFIVGRYVQF/", "filename": "galGal5.bwaIndex.tgz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "bwaIndex", "uuid": "d13d06cf-218e-4f61-55f0-91f226248b2c", "display_title": "bwaIndex", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/bwaIndex/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"workflow_argument_name": "fastq1", "value": {"status": "released", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIVCCTJCI.fastq.gz", "uuid": "53ccd95f-03eb-4c56-8547-52a423f2da28", "accession": "4DNFIVCCTJCI", "@id": "/files-fastq/4DNFIVCCTJCI/", "filename": "SRR5939681_1.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"workflow_argument_name": "fastq2", "value": {"status": "released", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIXV4QI5Z.fastq.gz", "uuid": "dea8d5cd-60fe-436f-bbb0-d65d6e217e1c", "accession": "4DNFIXV4QI5Z", "@id": "/files-fastq/4DNFIXV4QI5Z/", "filename": "SRR5939681_2.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "workflow": {"display_title": "Alignment for Hi-C using bwa-mem 0.2.6 - 4DNWF84NFOQP", "title": "Alignment for Hi-C using bwa-mem 0.2.6", "@type": ["Workflow", "Item"], "@id": "/workflows/4DNWF84NFOQP/", "status": "released", "uuid": "3feedadc-50f9-4bb4-919b-09a8b731d0cc", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "@id": "/workflow-runs-awsem/5beedf5e-54b7-4038-a76a-015ee3ce098d/", "status": "released", "uuid": "5beedf5e-54b7-4038-a76a-015ee3ce098d", "display_title": "fastq-first-line v2 run 2020-04-08 06:15:52.311819", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "output_files": [{"workflow_argument_name": "first_line"}], "input_files": [{"workflow_argument_name": "fastq", "value": {"status": "released", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIXV4QI5Z.fastq.gz", "uuid": "dea8d5cd-60fe-436f-bbb0-d65d6e217e1c", "accession": "4DNFIXV4QI5Z", "@id": "/files-fastq/4DNFIXV4QI5Z/", "filename": "SRR5939681_2.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "workflow": {"display_title": "Getting first line of fastq file - 4DNWFASTQFO1", "title": "Getting first line of fastq file", "@type": ["Workflow", "Item"], "@id": "/workflows/4DNWFASTQFO1/", "status": "released", "uuid": "93a1a931-d55d-4623-adfb-0fa735daf6ae", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow_run_outputs": [], "@context": "/terms/", "aggregated-items": {}, "validation-errors": []}