{"lab": {"status": "current", "display_title": "Rafael Casellas, NIH", "correspondence": [{"contact_email": "Y2FzZWxsYXJAbWFpbC5uaWguZ292", "@id": "/users/68b09572-0c3e-48c7-90a9-7bad21d6bac1/", "display_title": "Rafael Casellas"}], "uuid": "ce54a7f7-af8a-4505-8327-e430634f494b", "title": "Rafael Casellas, NIH", "@id": "/labs/rafael-casellas-lab/", "@type": ["Lab", "Item"], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.ce54a7f7-af8a-4505-8327-e430634f494b"]}}, "award": {"status": "current", "name": "external-award", "description": "Funding source is from outside 4DN.", "@id": "/awards/external-award/", "center_title": "External", "uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "@type": ["Award", "Item"], "project": "External", "display_title": "EXTERNAL AWARD", "center": "External", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "f2eb90ff579ecade8b02664918b482ad", "status": "released", "aliases": ["4dn-dcic-lab:SRR7142917_2_fq"], "dbxrefs": ["SRA:SRR7142917"], "filename": "SRR7142917_2.fastq.gz", "accession": "4DNFIMOHTR3N", "file_size": 6350561, "file_type": "reads", "instrument": "Illumina HiSeq 2500", "paired_end": "2", "description": "SRA:SRR7142917 from Vian et. al, GEO:GSE98119", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "display_title": "fastq", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "read_length": 100, "date_created": "2018-11-27T17:52:28.347365+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2020-04-08T03:51:53.833972+00:00"}, "related_files": [{"file": {"@type": ["FileFastq", "File", "Item"], "status": "released", "uuid": "d2d84554-615f-42b5-92bf-7cb3b865b469", "display_title": "4DNFIB7TQZA7.fastq.gz", "accession": "4DNFIB7TQZA7", "@id": "/files-fastq/4DNFIB7TQZA7/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "relationship_type": "paired with"}], "content_md5sum": "140369763f42f9ef64fe20f3beeed824", "public_release": "2019-11-25", "quality_metric": {"@id": "/quality-metrics-fastqc/a851b6a0-ed03-4ac0-bf65-f97434816da4/", "uuid": "a851b6a0-ed03-4ac0-bf65-f97434816da4", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "overall_quality_status": "PASS", "status": "released", "Sequence length": "100", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIMOHTR3N/fastqc_report.html", "display_title": "QualityMetricFastqc from 2018-11-28", "Total Sequences": 68827, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "schema_version": "2", "file_first_line": "@DFXGT8Q1:348:C6Y35ACXX:4:1101:14994:2071", "project_release": "2019-11-25", "file_classification": "raw file", "@id": "/files-fastq/4DNFIMOHTR3N/", "@type": ["FileFastq", "File", "Item"], "uuid": "902780df-94db-47a1-802b-759d00657a5a", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNFIMOHTR3N.fastq.gz", "external_references": [{"ref": "SRA:SRR7142917", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR7142917"}], "experiments": [{"display_title": "in situ Hi-C on CH12 with MboI - 4DNEXA51AJL6", "status": "released", "@id": "/experiments-hi-c/4DNEXA51AJL6/", "@type": ["ExperimentHiC", "Experiment", "Item"], "accession": "4DNEXA51AJL6", "uuid": "e1e5d8f8-3d1a-41f3-8aa3-29e5c8a11576", "biosample": {"biosource_summary": "CH12", "@type": ["Biosample", "Item"], "uuid": "28e4be1a-c7a3-42c5-876f-7ab4139aac6f", "@id": "/biosamples/4DNBS1AJKASN/", "status": "released", "modifications_summary": "Crispr generated targeted CTCF point mutations", "display_title": "4DNBS1AJKASN", "accession": "4DNBS1AJKASN", "treatments_summary": "None", "biosource": [{"biosource_type": "immortalized cell line", "cell_line_tier": "Unclassified", "status": "released", "@id": "/biosources/4DNSRPNYPN22/", "@type": ["Biosource", "Item"], "uuid": "5c4f486e-4f36-4d57-a38a-966e0ea29716", "display_title": "CH12 - 4DNSRPNYPN22", "tissue": {"term_name": "lymphocyte of B lineage", "preferred_name": "B-lymphocyte", "@type": ["OntologyTerm", "Item"], "term_id": "CL:0000945", "display_title": "B-lymphocyte", "status": "released", "uuid": "0c98ef0b-9a03-43f3-b409-fb091e62e2f8", "@id": "/ontology-terms/CL:0000945/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "cell_line": {"display_title": "CH12", "preferred_name": "CH12", "@id": "/ontology-terms/4DN:0000263/", "status": "released", "term_name": "CH12", "uuid": "8647e451-5e4c-41d1-98b6-b3c57226fbb3", "@type": ["OntologyTerm", "Item"], "term_id": "4DN:0000263", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"status": "released", "scientific_name": "Mus musculus", "name": "mouse", "display_title": "M. musculus", "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "@type": ["Organism", "Item"], "@id": "/organisms/10090/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"@type": ["IndividualMouse", "Individual", "Item"], "display_title": "4DNINGX2D3T7", "status": "released", "uuid": "a247155e-e826-464e-ae9a-ac1f0017af64", "@id": "/individuals-mouse/4DNINGX2D3T7/", "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": {"display_title": "MboI", "@type": ["Enzyme", "Item"], "status": "released", "@id": "/enzymes/MboI/", "uuid": "d8da42d0-bc20-40e5-bacf-c263b8603e03", "name": "MboI", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2024-07-15T20:36:56.144132+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "experiment_type": {"title": "in situ Hi-C", "@type": ["ExperimentType", "Item"], "display_title": "in situ Hi-C", "uuid": "a2920a38-cdba-4ff0-b4f0-c6bb53257747", "status": "released", "@id": "/experiment-types/in-situ-hi-c/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_sets": [{"status": "released", "uuid": "47beac46-2696-4031-ae99-51608bf7c3d3", "display_title": "4DNES4GDH4BG", "experimentset_type": "replicate", "accession": "4DNES4GDH4BG", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "@id": "/experiment-set-replicates/4DNES4GDH4BG/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}], "file_type_detailed": "reads (fastq)", "track_and_facet_info": {"experimental_lab": "Rafael Casellas, NIH", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "MboI", "dataset": "Hi-C on CH12 +/- CTCF ZF domain", "condition": "CTCF Zinc Finger Exon9-11 mutation", "replicate_info": "Biorep 16, Techrep 1", "biosource_name": "CH12", "lab_name": "Rafael Casellas, NIH"}, "title": "4DNFIMOHTR3N", "href": "/files-fastq/4DNFIMOHTR3N/@@download/4DNFIMOHTR3N.fastq.gz", "upload_key": "902780df-94db-47a1-802b-759d00657a5a/4DNFIMOHTR3N.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/902780df-94db-47a1-802b-759d00657a5a/4DNFIMOHTR3N.fastq.gz", "tsv_notes": "", "workflow_run_inputs": [{"@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "uuid": "d4328c7f-446f-41fa-b901-feff57efb959", "status": "released", "@id": "/workflow-runs-awsem/d4328c7f-446f-41fa-b901-feff57efb959/", "display_title": "md5 0.2.6 run 2018-11-28 00:18:02.918316", "input_files": [{"workflow_argument_name": "input_file", "value": {"status": "released", "uuid": "902780df-94db-47a1-802b-759d00657a5a", "accession": "4DNFIMOHTR3N", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIMOHTR3N.fastq.gz", "filename": "SRR7142917_2.fastq.gz", "@id": "/files-fastq/4DNFIMOHTR3N/", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "fastq", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"display_title": "md5 0.2.6 - 4DNWF2HFF82B", "uuid": "c77a117b-9a58-477e-aaa5-291a109a99f6", "status": "released", "title": "md5 0.2.6", "@id": "/workflows/4DNWF2HFF82B/", "@type": ["Workflow", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "output_files": [{"workflow_argument_name": "report"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "uuid": "67203035-1e86-426a-b62b-d4a77d3f7d41", "status": "released", "@id": "/workflow-runs-awsem/67203035-1e86-426a-b62b-d4a77d3f7d41/", "display_title": "fastqc v1 run 2018-11-28 03:15:45.175415", "input_files": [{"workflow_argument_name": "input_fastq", "value": {"status": "released", "uuid": "902780df-94db-47a1-802b-759d00657a5a", "accession": "4DNFIMOHTR3N", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIMOHTR3N.fastq.gz", "filename": "SRR7142917_2.fastq.gz", "@id": "/files-fastq/4DNFIMOHTR3N/", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "fastq", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"display_title": "FastQC v1 - 4DNWFAW5VTA5", "uuid": "2324ad76-ff37-4157-8bcc-3ce72b7dace9", "status": "released", "title": "FastQC v1", "@id": "/workflows/4DNWFAW5VTA5/", "@type": ["Workflow", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "output_files": [{"workflow_argument_name": "report_zip", "value_qc": {"uuid": "a851b6a0-ed03-4ac0-bf65-f97434816da4", "status": "released", "@id": "/quality-metrics-fastqc/a851b6a0-ed03-4ac0-bf65-f97434816da4/", "overall_quality_status": "PASS", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIMOHTR3N/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "display_title": "QualityMetricFastqc from 2018-11-28", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "uuid": "e055abfb-213b-4aa2-963f-f9aa05c7411c", "status": "released", "@id": "/workflow-runs-awsem/e055abfb-213b-4aa2-963f-f9aa05c7411c/", "display_title": "bwa-mem 0.2.6 run 2018-11-30 09:51:06.451043", "input_files": [{"workflow_argument_name": "bwa_index", "value": {"status": "released", "uuid": "4a6d10ee-2edb-4402-a98f-0edb1d58f5e1", "accession": "4DNFI823LSI8", "@type": ["FileReference", "File", "Item"], "display_title": "4DNFI823LSI8.bwaIndex.tgz", "filename": "mm10.bwaIndex.tgz", "@id": "/files-reference/4DNFI823LSI8/", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bwaIndex", "@id": "/file-formats/bwaIndex/", "uuid": "d13d06cf-218e-4f61-55f0-91f226248b2c", "status": "released", "file_format": "bwaIndex", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "fastq1", "value": {"status": "released", "uuid": "d2d84554-615f-42b5-92bf-7cb3b865b469", "accession": "4DNFIB7TQZA7", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIB7TQZA7.fastq.gz", "filename": "SRR7142917_1.fastq.gz", "@id": "/files-fastq/4DNFIB7TQZA7/", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "fastq", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "fastq2", "value": {"status": "released", "uuid": "902780df-94db-47a1-802b-759d00657a5a", "accession": "4DNFIMOHTR3N", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIMOHTR3N.fastq.gz", "filename": "SRR7142917_2.fastq.gz", "@id": "/files-fastq/4DNFIMOHTR3N/", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "fastq", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"display_title": "Alignment for Hi-C using bwa-mem 0.2.6 - 4DNWF84NFOQP", "uuid": "3feedadc-50f9-4bb4-919b-09a8b731d0cc", "status": "released", "title": "Alignment for Hi-C using bwa-mem 0.2.6", "@id": "/workflows/4DNWF84NFOQP/", "@type": ["Workflow", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "output_files": [{"workflow_argument_name": "out_bam", "value": {"status": "released", "accession": "4DNFIFWB2BQ4", "@id": "/files-processed/4DNFIFWB2BQ4/", "uuid": "475540f8-96f2-4d84-bb38-eaf7a9a92174", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIFWB2BQ4.bam", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "file_format": "bam", "@id": "/file-formats/bam/", "@type": ["FileFormat", "Item"], "display_title": "bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "uuid": "70679a20-b715-4c0f-b9d6-253486395ed3", "status": "released", "@id": "/workflow-runs-awsem/70679a20-b715-4c0f-b9d6-253486395ed3/", "display_title": "fastq-first-line v2 run 2020-04-08 03:46:40.866237", "input_files": [{"workflow_argument_name": "fastq", "value": {"status": "released", "uuid": "902780df-94db-47a1-802b-759d00657a5a", "accession": "4DNFIMOHTR3N", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIMOHTR3N.fastq.gz", "filename": "SRR7142917_2.fastq.gz", "@id": "/files-fastq/4DNFIMOHTR3N/", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "fastq", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"display_title": "Getting first line of fastq file - 4DNWFASTQFO1", "uuid": "93a1a931-d55d-4623-adfb-0fa735daf6ae", "status": "released", "title": "Getting first line of fastq file", "@id": "/workflows/4DNWFASTQFO1/", "@type": ["Workflow", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "output_files": [{"workflow_argument_name": "first_line"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "workflow_run_outputs": [], "@context": "/terms/", "aggregated-items": {}, "validation-errors": []}