{"lab": {"@type": ["Lab", "Item"], "@id": "/labs/benjamin-rowland-lab/", "status": "current", "title": "Benjamin Rowland, NKI", "display_title": "Benjamin Rowland, NKI", "uuid": "6e1ac73e-bdb7-4995-b003-2c31f538049a", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6e1ac73e-bdb7-4995-b003-2c31f538049a"]}}, "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": "c117f0c56b25ca8dae2945dcaa26b6c7", "status": "released", "aliases": ["4dn-dcic-lab:SRR5266590_2_fq"], "dbxrefs": ["SRA:SRR5266590"], "filename": "SRR5266590_2.fastq.gz", "accession": "4DNFI2MORRN3", "file_size": 41981059467, "file_type": "reads", "instrument": "HiSeq X Ten", "paired_end": "2", "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": 150, "date_created": "2018-10-17T20:56:59.698955+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2020-04-09T00:54:34.774511+00:00"}, "related_files": [{"file": {"accession": "4DNFIIWQM7IR", "uuid": "3dee2535-9219-42d5-8272-559d71020bb2", "display_title": "4DNFIIWQM7IR.fastq.gz", "@type": ["FileFastq", "File", "Item"], "status": "released", "@id": "/files-fastq/4DNFIIWQM7IR/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "relationship_type": "paired with"}], "content_md5sum": "f4b20d31d7a8a11590be2e29dee853c4", "public_release": "2018-12-06", "quality_metric": {"display_title": "QualityMetricFastqc from 2018-11-17", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "4eb5e203-a78a-4159-b24e-ae2a14c9d0c3", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI2MORRN3/fastqc_report.html", "status": "released", "overall_quality_status": "PASS", "Total Sequences": 486704798, "Sequence length": "150", "@id": "/quality-metrics-fastqc/4eb5e203-a78a-4159-b24e-ae2a14c9d0c3/", "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/4DNFI2MORRN3/", "@type": ["FileFastq", "File", "Item"], "uuid": "1f267e3c-7391-4a3a-8420-beb9fa4e7932", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNFI2MORRN3.fastq.gz", "external_references": [{"ref": "SRA:SRR5266590", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5266590"}], "experiments": [{"@id": "/experiments-hi-c/4DNEXUYGDZDK/", "uuid": "33e751be-2042-48c5-8fd4-5a9d10d4d71b", "@type": ["ExperimentHiC", "Experiment", "Item"], "display_title": "in situ Hi-C on HAP-1 with MboI - 4DNEXUYGDZDK", "status": "released", "accession": "4DNEXUYGDZDK", "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": "4DNBSOLYNBQA", "status": "released", "uuid": "44ab68ba-b17d-4713-ad88-e9c5a192a620", "@id": "/biosamples/4DNBSOLYNBQA/", "accession": "4DNBSOLYNBQA", "modifications_summary": "Crispr deletion of SCC4", "treatments_summary": "None", "biosource_summary": "HAP-1", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "biosource": [{"@type": ["Biosource", "Item"], "status": "released", "biosource_type": "immortalized cell line", "display_title": "HAP-1 - 4DNSRNIAESOK", "uuid": "18fc203e-0b65-43b7-8373-0c8fdf5eff57", "@id": "/biosources/4DNSRNIAESOK/", "cell_line_tier": "Unclassified", "modifications": [], "organism": {"status": "released", "name": "human", "@id": "/organisms/9606/", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "@type": ["Organism", "Item"], "display_title": "H. sapiens", "scientific_name": "Homo sapiens", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "cell_line": {"preferred_name": "HAP-1", "@type": ["OntologyTerm", "Item"], "term_name": "HAP-1", "display_title": "HAP-1", "@id": "/ontology-terms/EFO:0007598/", "uuid": "57d18eec-d662-4bf7-8000-047de03ad84a", "term_id": "EFO:0007598", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"@type": ["OntologyTerm", "Item"], "status": "released", "term_name": "blood cell", "uuid": "0d64fbe2-ed5c-43cd-a30d-d9f0320d27ed", "term_id": "CL:0000081", "preferred_name": "blood cell", "@id": "/ontology-terms/CL:0000081/", "display_title": "blood cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"@id": "/individuals-human/4DNINGLJ7A6Z/", "@type": ["IndividualHuman", "Individual", "Item"], "display_title": "4DNINGLJ7A6Z", "protected_data": false, "uuid": "6e37c213-33dd-4aff-aedb-b466a4b2aa45", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, "digestion_enzyme": {"uuid": "d8da42d0-bc20-40e5-bacf-c263b8603e03", "display_title": "MboI", "@type": ["Enzyme", "Item"], "status": "released", "@id": "/enzymes/MboI/", "name": "MboI", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_sets": [{"experimentset_type": "replicate", "@id": "/experiment-set-replicates/4DNESNLXBFMY/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "9094ec5b-1e2d-4c2c-bb38-e6e5b0222ce9", "accession": "4DNESNLXBFMY", "status": "released", "display_title": "4DNESNLXBFMY", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2024-07-19T13:22:11.542200+00:00"}}], "file_type_detailed": "reads (fastq)", "track_and_facet_info": {"experimental_lab": "Benjamin Rowland, NKI", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "MboI", "dataset": "Hi-C on HAP-1 +/- WAPL or SCC4 KO", "condition": "SCC4 knock out", "replicate_info": "Biorep 1, Techrep 2", "biosource_name": "HAP-1", "lab_name": "Benjamin Rowland, NKI"}, "title": "4DNFI2MORRN3", "href": "/files-fastq/4DNFI2MORRN3/@@download/4DNFI2MORRN3.fastq.gz", "upload_key": "1f267e3c-7391-4a3a-8420-beb9fa4e7932/4DNFI2MORRN3.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/1f267e3c-7391-4a3a-8420-beb9fa4e7932/4DNFI2MORRN3.fastq.gz", "tsv_notes": "", "workflow_run_inputs": [{"display_title": "md5 0.2.6 run 2018-11-17 01:03:41.880872", "@id": "/workflow-runs-awsem/11884c1f-bd36-4042-9e47-fd31104a2da3/", "status": "released", "uuid": "11884c1f-bd36-4042-9e47-fd31104a2da3", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "output_files": [{"workflow_argument_name": "report"}], "input_files": [{"workflow_argument_name": "input_file", "value": {"accession": "4DNFI2MORRN3", "filename": "SRR5266590_2.fastq.gz", "display_title": "4DNFI2MORRN3.fastq.gz", "@id": "/files-fastq/4DNFI2MORRN3/", "@type": ["FileFastq", "File", "Item"], "status": "released", "uuid": "1f267e3c-7391-4a3a-8420-beb9fa4e7932", "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 2018-11-17 01:03:45.642711", "@id": "/workflow-runs-awsem/d16f7043-4708-4f67-9124-0d0df38d27c4/", "status": "released", "uuid": "d16f7043-4708-4f67-9124-0d0df38d27c4", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "output_files": [{"workflow_argument_name": "report_zip", "value_qc": {"display_title": "QualityMetricFastqc from 2018-11-17", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI2MORRN3/fastqc_report.html", "status": "released", "uuid": "4eb5e203-a78a-4159-b24e-ae2a14c9d0c3", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/4eb5e203-a78a-4159-b24e-ae2a14c9d0c3/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "input_files": [{"workflow_argument_name": "input_fastq", "value": {"accession": "4DNFI2MORRN3", "filename": "SRR5266590_2.fastq.gz", "display_title": "4DNFI2MORRN3.fastq.gz", "@id": "/files-fastq/4DNFI2MORRN3/", "@type": ["FileFastq", "File", "Item"], "status": "released", "uuid": "1f267e3c-7391-4a3a-8420-beb9fa4e7932", "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 2018-11-21 15:25:22.577740", "@id": "/workflow-runs-awsem/39ade0b3-a6f0-4167-b9f5-1abecd20c062/", "status": "released", "uuid": "39ade0b3-a6f0-4167-b9f5-1abecd20c062", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "output_files": [{"workflow_argument_name": "out_bam", "value": {"status": "released", "uuid": "7e3e51cd-efe9-4d4e-bd8a-7559998e8570", "display_title": "4DNFIPP2GCL2.bam", "@id": "/files-processed/4DNFIPP2GCL2/", "accession": "4DNFIPP2GCL2", "@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": "4DNFIZQZ39L9", "filename": "hg38.bwaIndex.tgz", "display_title": "4DNFIZQZ39L9.bwaIndex.tgz", "@id": "/files-reference/4DNFIZQZ39L9/", "@type": ["FileReference", "File", "Item"], "status": "released", "uuid": "1f53df95-4cf3-41cc-971d-81bb16c486dd", "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": "4DNFIIWQM7IR", "filename": "SRR5266590_1.fastq.gz", "display_title": "4DNFIIWQM7IR.fastq.gz", "@id": "/files-fastq/4DNFIIWQM7IR/", "@type": ["FileFastq", "File", "Item"], "status": "released", "uuid": "3dee2535-9219-42d5-8272-559d71020bb2", "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": "4DNFI2MORRN3", "filename": "SRR5266590_2.fastq.gz", "display_title": "4DNFI2MORRN3.fastq.gz", "@id": "/files-fastq/4DNFI2MORRN3/", "@type": ["FileFastq", "File", "Item"], "status": "released", "uuid": "1f267e3c-7391-4a3a-8420-beb9fa4e7932", "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 2020-04-09 00:49:19.583527", "@id": "/workflow-runs-awsem/d59064ef-5f32-45e9-a53c-baeb26a4bcbf/", "status": "released", "uuid": "d59064ef-5f32-45e9-a53c-baeb26a4bcbf", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "output_files": [{"workflow_argument_name": "first_line"}], "input_files": [{"workflow_argument_name": "fastq", "value": {"accession": "4DNFI2MORRN3", "filename": "SRR5266590_2.fastq.gz", "display_title": "4DNFI2MORRN3.fastq.gz", "@id": "/files-fastq/4DNFI2MORRN3/", "@type": ["FileFastq", "File", "Item"], "status": "released", "uuid": "1f267e3c-7391-4a3a-8420-beb9fa4e7932", "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": []}