{"lab": {"correspondence": [{"contact_email": "Y2FzZWxsYXJAbWFpbC5uaWguZ292", "@id": "/users/68b09572-0c3e-48c7-90a9-7bad21d6bac1/", "display_title": "Rafael Casellas"}], "uuid": "ce54a7f7-af8a-4505-8327-e430634f494b", "@id": "/labs/rafael-casellas-lab/", "status": "current", "title": "Rafael Casellas, NIH", "display_title": "Rafael Casellas, NIH", "@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": {"uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "@id": "/awards/external-award/", "center": "External", "@type": ["Award", "Item"], "display_title": "EXTERNAL AWARD", "name": "external-award", "description": "Funding source is from outside 4DN.", "center_title": "External", "project": "External", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "e073eb24f49d51772713afd83828bb14", "status": "released", "aliases": ["4dn-dcic-lab:SRR6794600_fq"], "dbxrefs": ["SRA:SRR6794600"], "filename": "SRR6794600.fastq.gz", "accession": "4DNFIZCD6MNT", "file_size": 1085708720, "file_type": "reads", "instrument": "Illumina HiSeq 3000", "description": "SRA:SRR6794600 from Vian et. al, GEO:GSE98119", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "status": "released", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "read_length": 49, "date_created": "2018-11-27T17:44:41.354675+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2020-04-08T05:17:49.498026+00:00"}, "content_md5sum": "ed36b0077948bfadb356baa862d84e53", "public_release": "2019-12-02", "quality_metric": {"Total Sequences": 37158017, "display_title": "QualityMetricFastqc from 2018-11-27", "Sequence length": "35-50", "@id": "/quality-metrics-fastqc/1ebe6816-df18-4082-9117-8a9614c4b40d/", "overall_quality_status": "PASS", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIZCD6MNT/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "1ebe6816-df18-4082-9117-8a9614c4b40d", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "schema_version": "2", "file_first_line": "@1", "project_release": "2019-12-02", "file_classification": "raw file", "@id": "/files-fastq/4DNFIZCD6MNT/", "@type": ["FileFastq", "File", "Item"], "uuid": "ee0f0046-87cc-4228-85fc-1dc68d7ba2a7", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNFIZCD6MNT.fastq.gz", "external_references": [{"ref": "SRA:SRR6794600", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR6794600"}], "experiments": [{"status": "released", "@type": ["ExperimentSeq", "Experiment", "Item"], "uuid": "0be36f27-4592-426e-8862-94907ee5ac3a", "display_title": "ChIP-seq against Nipbl mouse protein on B cell derived cell line - 4DNEXBBUQAES", "accession": "4DNEXBBUQAES", "@id": "/experiments-seq/4DNEXBBUQAES/", "biosample": {"@type": ["Biosample", "Item"], "status": "released", "@id": "/biosamples/4DNBS6IUUI16/", "modifications_summary": "None", "accession": "4DNBS6IUUI16", "treatments_summary": "LPS (Sigma) treatment (50.0 \u03bcg/mL, 30.0h) and IL-4 (Sigma) treatment (2.5 ng/mL, 30.0h) and anti-CD180 (RP105) antibody, BD PharMingen treatment (0.5 \u03bcg/mL, 30.0h)", "uuid": "53cd7260-b43a-43d6-abad-fc6695f81c86", "biosource_summary": "B cell derived cell line", "display_title": "4DNBS6IUUI16", "biosource": [{"@id": "/biosources/4DNSRA3JY5KY/", "uuid": "469a5e58-d40f-4536-8df9-5c603111ba1f", "status": "released", "biosource_type": "primary cell", "@type": ["Biosource", "Item"], "display_title": "B cell derived cell line - 4DNSRA3JY5KY", "cell_line_tier": "Unclassified", "tissue": {"display_title": "splenocyte", "@id": "/ontology-terms/CL:2000074/", "preferred_name": "splenocyte", "status": "released", "term_name": "splenocyte", "uuid": "94bbfc93-633a-450a-92d9-261c13d3548a", "@type": ["OntologyTerm", "Item"], "term_id": "CL:2000074", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "organism": {"@type": ["Organism", "Item"], "name": "mouse", "display_title": "M. musculus", "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "status": "released", "@id": "/organisms/10090/", "scientific_name": "Mus musculus", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"status": "released", "@type": ["IndividualMouse", "Individual", "Item"], "uuid": "408b84a5-aaa6-4d79-81d8-c3b6ba280f49", "@id": "/individuals-mouse/4DNIN9IKCB4R/", "display_title": "4DNIN9IKCB4R", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "cell_line": {"term_name": "B cell derived cell line", "display_title": "B cell derived cell line", "term_id": "EFO:0001640", "status": "released", "@id": "/ontology-terms/EFO:0001640/", "uuid": "a35ee804-9776-45b2-8b66-d29b00558c8d", "@type": ["OntologyTerm", "Item"], "preferred_name": "B cell derived cell line", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_type": {"@id": "/experiment-types/chip-seq/", "display_title": "ChIP-seq", "status": "released", "title": "ChIP-seq", "uuid": "47a593da-c458-422a-a974-82b3302e89cb", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_sets": [{"experimentset_type": "replicate", "display_title": "4DNESRQNIDYZ", "accession": "4DNESRQNIDYZ", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "b5afaa85-3f65-4db7-abac-31222e0881a2", "status": "released", "@id": "/experiment-set-replicates/4DNESRQNIDYZ/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2019-12-02T01:08:40.568206+00:00"}}], "file_type_detailed": "reads (fastq)", "track_and_facet_info": {"experimental_lab": "Rafael Casellas, NIH", "experiment_type": "ChIP-seq", "experiment_bucket": "raw file", "assay_info": "Nipbl mouse protein", "dataset": "ChIP-seq on activated B cells", "condition": "anti-Nipbl", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "B cell derived cell line", "lab_name": "Rafael Casellas, NIH"}, "title": "4DNFIZCD6MNT", "href": "/files-fastq/4DNFIZCD6MNT/@@download/4DNFIZCD6MNT.fastq.gz", "upload_key": "ee0f0046-87cc-4228-85fc-1dc68d7ba2a7/4DNFIZCD6MNT.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/ee0f0046-87cc-4228-85fc-1dc68d7ba2a7/4DNFIZCD6MNT.fastq.gz", "tsv_notes": "", "workflow_run_inputs": [{"@id": "/workflow-runs-awsem/a5e1be1b-7575-4d08-a79f-281c429d1fab/", "status": "released", "display_title": "fastqc v1 run 2018-11-27 19:17:13.189484", "uuid": "a5e1be1b-7575-4d08-a79f-281c429d1fab", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "input_files": [{"workflow_argument_name": "input_fastq", "value": {"status": "released", "accession": "4DNFIZCD6MNT", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIZCD6MNT/", "display_title": "4DNFIZCD6MNT.fastq.gz", "filename": "SRR6794600.fastq.gz", "uuid": "ee0f0046-87cc-4228-85fc-1dc68d7ba2a7", "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"@type": ["Workflow", "Item"], "title": "FastQC v1", "status": "released", "@id": "/workflows/4DNWFAW5VTA5/", "display_title": "FastQC v1 - 4DNWFAW5VTA5", "uuid": "2324ad76-ff37-4157-8bcc-3ce72b7dace9", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "output_files": [{"workflow_argument_name": "report_zip", "value_qc": {"uuid": "1ebe6816-df18-4082-9117-8a9614c4b40d", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIZCD6MNT/fastqc_report.html", "status": "released", "@id": "/quality-metrics-fastqc/1ebe6816-df18-4082-9117-8a9614c4b40d/", "display_title": "QualityMetricFastqc from 2018-11-27", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "overall_quality_status": "PASS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/workflow-runs-awsem/a4779525-6c17-4758-bcf9-204e21ab4f45/", "status": "released", "display_title": "md5 0.2.6 run 2018-11-27 19:17:19.498556", "uuid": "a4779525-6c17-4758-bcf9-204e21ab4f45", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "input_files": [{"workflow_argument_name": "input_file", "value": {"status": "released", "accession": "4DNFIZCD6MNT", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIZCD6MNT/", "display_title": "4DNFIZCD6MNT.fastq.gz", "filename": "SRR6794600.fastq.gz", "uuid": "ee0f0046-87cc-4228-85fc-1dc68d7ba2a7", "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"@type": ["Workflow", "Item"], "title": "md5 0.2.6", "status": "released", "@id": "/workflows/4DNWF2HFF82B/", "display_title": "md5 0.2.6 - 4DNWF2HFF82B", "uuid": "c77a117b-9a58-477e-aaa5-291a109a99f6", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "output_files": [{"workflow_argument_name": "report"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/workflow-runs-awsem/9816e67b-fd9f-4cb6-9ccf-24a255f9005f/", "status": "released", "display_title": "encode-chipseq-aln-chip 1.1.1 run 2019-06-18 15:21:27.529201", "uuid": "9816e67b-fd9f-4cb6-9ccf-24a255f9005f", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "input_files": [{"workflow_argument_name": "chip.bwa_idx_tar", "value": {"status": "released", "accession": "4DNFIZ2PWCC2", "@type": ["FileReference", "File", "Item"], "@id": "/files-reference/4DNFIZ2PWCC2/", "display_title": "4DNFIZ2PWCC2.bwaIndex.tar", "filename": "mm10.bwaIndex.tar", "uuid": "f4b63d31-65d8-437f-a76a-6bedbb52ae6f", "file_format": {"@id": "/file-formats/uncompressed_bwaIndex/", "file_format": "uncompressed_bwaIndex", "status": "released", "@type": ["FileFormat", "Item"], "display_title": "uncompressed_bwaIndex", "uuid": "96809e57-4ccd-40b4-9fcb-ce27c4f16df9", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "chip.blacklist", "value": {"status": "released", "accession": "4DNFIZ3FBPK8", "@type": ["FileReference", "File", "Item"], "@id": "/files-reference/4DNFIZ3FBPK8/", "display_title": "4DNFIZ3FBPK8.bed.gz", "filename": "mm10.blacklist.bed.gz", "uuid": "a32747a3-8a9e-4a9e-a7a1-4db0e8b65925", "file_format": {"@id": "/file-formats/bed/", "file_format": "bed", "status": "released", "@type": ["FileFormat", "Item"], "display_title": "bed", "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "chip.chrsz", "value": {"status": "released", "accession": "4DNFIBP173GC", "@type": ["FileReference", "File", "Item"], "@id": "/files-reference/4DNFIBP173GC/", "display_title": "4DNFIBP173GC.chrom.sizes", "filename": "mm10_no_alt.chrom.sizes", "uuid": "be0a9819-d2ce-4422-be4b-234fb1677dd9", "file_format": {"@id": "/file-formats/chromsizes/", "file_format": "chromsizes", "status": "released", "@type": ["FileFormat", "Item"], "display_title": "chromsizes", "uuid": "d13d06cf-218e-4f61-55f0-93f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "chip.fastqs", "value": {"status": "released", "accession": "4DNFIZCD6MNT", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIZCD6MNT/", "display_title": "4DNFIZCD6MNT.fastq.gz", "filename": "SRR6794600.fastq.gz", "uuid": "ee0f0046-87cc-4228-85fc-1dc68d7ba2a7", "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"@type": ["Workflow", "Item"], "title": "Chip-seq data processing pipeline, Align-only, ChIP 1.1.1", "status": "released", "@id": "/workflows/4DNWF25VHY99/", "display_title": "Chip-seq data processing pipeline, Align-only, ChIP 1.1.1 - 4DNWF25VHY99", "uuid": "1dfb78e8-9844-48c6-804e-d05e7257e178", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "output_files": [{"workflow_argument_name": "chip.first_ta", "value_qc": {"uuid": "ff28025a-6156-4c91-afb3-06aaa059ee23", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI3OLIHIZqc_report.html", "status": "released", "@id": "/quality-metrics-chipseq/ff28025a-6156-4c91-afb3-06aaa059ee23/", "display_title": "QualityMetricChipseq from 2019-06-18", "@type": ["QualityMetricChipseq", "QualityMetric", "Item"], "overall_quality_status": "PASS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "value": {"uuid": "65688b19-19d8-4458-af5a-75a03595012a", "display_title": "4DNFI3OLIHIZ.bed.gz", "accession": "4DNFI3OLIHIZ", "@id": "/files-processed/4DNFI3OLIHIZ/", "@type": ["FileProcessed", "File", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "bed", "file_format": "bed", "@id": "/file-formats/bed/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"workflow_argument_name": "chip.first_ta_xcor", "value": {"uuid": "89a0ed10-64d8-4d64-903e-70aa1a29a232", "display_title": "4DNFI6UDATL5.bed.gz", "accession": "4DNFI6UDATL5", "@id": "/files-processed/4DNFI6UDATL5/", "@type": ["FileProcessed", "File", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "bed", "file_format": "bed", "@id": "/file-formats/bed/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"workflow_argument_name": "chip.report"}, {"workflow_argument_name": "chip.qc_json"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/workflow-runs-awsem/0e2c063e-0ef0-4879-87f4-c14cd61c39b3/", "status": "released", "display_title": "fastq-first-line v2 run 2020-04-08 05:12:38.672082", "uuid": "0e2c063e-0ef0-4879-87f4-c14cd61c39b3", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "input_files": [{"workflow_argument_name": "fastq", "value": {"status": "released", "accession": "4DNFIZCD6MNT", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIZCD6MNT/", "display_title": "4DNFIZCD6MNT.fastq.gz", "filename": "SRR6794600.fastq.gz", "uuid": "ee0f0046-87cc-4228-85fc-1dc68d7ba2a7", "file_format": {"@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"@type": ["Workflow", "Item"], "title": "Getting first line of fastq file", "status": "released", "@id": "/workflows/4DNWFASTQFO1/", "display_title": "Getting first line of fastq file - 4DNWFASTQFO1", "uuid": "93a1a931-d55d-4623-adfb-0fa735daf6ae", "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": []}