{"lab": {"display_title": "Karen Adelman, HARVARD", "correspondence": [{"contact_email": "a2FyZW5fYWRlbG1hbkBobXMuaGFydmFyZC5lZHU=", "@id": "/users/59826b1d-7f8b-484f-bfba-8e29f57169d2/", "display_title": "Karen Adelman"}], "@type": ["Lab", "Item"], "title": "Karen Adelman, HARVARD", "@id": "/labs/karen-adelman-lab/", "status": "current", "uuid": "0aae4b45-b6de-45da-84e6-738667c36f03", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.0aae4b45-b6de-45da-84e6-738667c36f03"]}}, "award": {"@id": "/awards/TCPA-2017-01/", "name": "TCPA-2017-01", "uuid": "619535d9-ec49-4f36-9cad-a0887cf535cb", "description": "TCPA: \u200bThere is a clear relationship between nuclear genome organization and the regulation of gene expression, and a great deal of effort has been dedicated to defining the effects of genome architecture on gene activity. Herein, we propose to complement this work by approaching the relationship from the other direction. We will ask: how does nascent RNA synthesis from enhancers and promoters impact genome organization? Our specific hypothesis is that nascent RNA plays a central role in stabilizing transient promoter-enhancer contacts that occur within topologically-associated domains (TADs), and thus facilitates the communication between distal cis-regulatory regions. This idea is supported by recent demonstrations that nascent RNA can serve as a platform for the recruitment and retention of transcription factors and epigenetic modifiers. Accordingly, several studies have suggested roles for specific enhancer RNAs in the establishment or maintenance of three-dimensional (3D) enhancer-promoter loops and associated gene activity. However, a full appreciation for the role of nascent RNA synthesis on \ngenome structure will require a more rigorous, coordinated and comprehensive approach than has been carried out to date. We therefore propose a collaborative project within the framework of the 4D Nucleome network to address how enhancer and gene transcription impact chromosome organization.", "status": "current", "display_title": "ELUCIDATING THE ROLE OF NASCENT RNA IN ENHANCER-PROMOTER COMMUNICATION AND THREE-DIMENSIONAL GENOME ORGANIZATION", "project": "4DN", "center_title": "TCPA - Adelman", "@type": ["Award", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "pi": {"error": "no view permissions"}}, "md5sum": "25afd23fbd857479cd344d0680cbf9a1", "status": "released", "aliases": ["karen-adelman-lab:filefastq_EpiLCdiff_RNAseq_48hr_B1_T1_f2_r1"], "filename": "LIB034317_TRA00123258_R1.fastq.gz", "accession": "4DNFIK5FN5L8", "file_size": 1364164259, "file_type": "reads", "paired_end": "1", "file_format": {"file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "date_created": "2021-01-22T00:33:24.079086+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2023-08-07T21:27:34.028950+00:00"}, "related_files": [{"file": {"accession": "4DNFIXEVQYFN", "uuid": "0f8f4128-82ad-4c6f-b546-0d1f0c99224c", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIXEVQYFN/", "status": "released", "display_title": "4DNFIXEVQYFN.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "relationship_type": "paired with"}], "content_md5sum": "c5e5f62b26f767e51be2e36de8f5ec62", "public_release": "2023-06-28", "quality_metric": {"overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/13b51a0f-dd5d-4db6-b796-12b05dd47554/", "Sequence length": "80", "display_title": "QualityMetricFastqc from 2021-01-24", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIK5FN5L8/fastqc_report.html", "Total Sequences": 30332398, "uuid": "13b51a0f-dd5d-4db6-b796-12b05dd47554", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "schema_version": "2", "file_first_line": "@NB501715:229:H2Y7VBGX7:1:11101:3008:1036 1:N:0:CCGTCC", "project_release": "2023-06-28", "contributing_labs": [{"@type": ["Lab", "Item"], "@id": "/labs/joanna-wysocka-lab/", "correspondence": [{"contact_email": "d3lzb2NrYUBzdGFuZm9yZC5lZHU=", "@id": "/users/1cc9469d-ff0c-4ef0-b0c7-5ed4d0966a13/", "display_title": "Joanna Wysocka"}], "status": "current", "uuid": "88ba2aa9-321a-43a5-af1e-75fca4236907", "display_title": "Joanna Wysocka, STANFORD", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.88ba2aa9-321a-43a5-af1e-75fca4236907"]}, "pi": {"error": "no view permissions"}}], "file_classification": "raw file", "beta_actin_sense_count": 0, "beta_actin_antisense_count": 1190, "@id": "/files-fastq/4DNFIK5FN5L8/", "@type": ["FileFastq", "File", "Item"], "uuid": "19df9937-3d28-4f0a-b23c-ca50a05cdb0f", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNFIK5FN5L8.fastq.gz", "external_references": [], "experiments": [{"display_title": "RNA-seq on F121-9-CASTx129 (Tier 2) differentiated to epiblast cell - 4DNEXCON99HI", "uuid": "8b87b9f2-ae99-47bf-9732-6c251b3d1462", "status": "released", "@id": "/experiments-seq/4DNEXCON99HI/", "accession": "4DNEXCON99HI", "@type": ["ExperimentSeq", "Experiment", "Item"], "biosample": {"biosource_summary": "F121-9-CASTx129 (Tier 2) differentiated to epiblast cell", "modifications_summary": "None", "@type": ["Biosample", "Item"], "accession": "4DNBSZ19F5VE", "uuid": "add0b995-7282-4669-afb1-d8f5502ef45d", "treatments_summary": "None", "status": "released", "display_title": "4DNBSZ19F5VE", "@id": "/biosamples/4DNBSZ19F5VE/", "biosource": [{"@id": "/biosources/4DNSRMG5APUM/", "status": "released", "uuid": "f01caf67-dd73-40ae-9476-940f0762b9c2", "display_title": "F121-9-CASTx129 (Tier 2) - 4DNSRMG5APUM", "biosource_type": "stem cell derived cell line", "cell_line_tier": "Tier 2", "@type": ["Biosource", "Item"], "modifications": [], "individual": {"status": "released", "@id": "/individuals-mouse/4DNINSF32UE9/", "uuid": "cade1337-728d-4b5d-99f5-ed08b621cd7b", "display_title": "4DNINSF32UE9", "@type": ["IndividualMouse", "Individual", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "cell_line": {"status": "released", "term_name": "F121-9-CASTx129", "uuid": "111201bc-8535-4448-903e-854af460a233", "display_title": "F121-9-CASTx129", "preferred_name": "F121-9-CASTx129", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/4DN:0000002/", "term_id": "4DN:0000002", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"preferred_name": "stem cell", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "term_name": "stem cell", "term_id": "CL:0000034", "display_title": "stem cell", "status": "released", "@id": "/ontology-terms/CL:0000034/", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"status": "released", "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "display_title": "M. musculus", "@id": "/organisms/10090/", "name": "mouse", "@type": ["Organism", "Item"], "scientific_name": "Mus musculus", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "cell_culture_details": [{"@id": "/biosample-cell-cultures/315b0fb8-ae3f-462d-9c74-b8cccd24bb29/", "display_title": "BiosampleCellCulture from 2021-01-22", "uuid": "315b0fb8-ae3f-462d-9c74-b8cccd24bb29", "status": "released", "@type": ["BiosampleCellCulture", "Item"], "in_vitro_differentiated": "Yes", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_sets": [{"@id": "/experiment-set-replicates/4DNESCT6MOUD/", "experimentset_type": "replicate", "uuid": "86fc34d0-bd29-4c87-8715-07a445463bb7", "status": "released", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "display_title": "4DNESCT6MOUD", "accession": "4DNESCT6MOUD", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "last_modified": {"date_modified": "2023-06-28T14:47:56.982939+00:00"}, "experiment_type": {"status": "released", "uuid": "19f848e6-7c52-4b8b-8aa8-e82ea0a968ce", "display_title": "RNA-seq", "title": "RNA-seq", "@type": ["ExperimentType", "Item"], "@id": "/experiment-types/rna-seq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "file_type_detailed": "reads (fastq)", "track_and_facet_info": {"experimental_lab": "Karen Adelman, HARVARD", "experiment_type": "RNA-seq", "experiment_bucket": "raw file", "dataset": "RNA-seq time course of EpiLC differentiation", "condition": "48 h", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F121-9-CASTx129 (Tier 2) differentiated to epiblast cell", "lab_name": "Karen Adelman, HARVARD"}, "title": "4DNFIK5FN5L8", "href": "/files-fastq/4DNFIK5FN5L8/@@download/4DNFIK5FN5L8.fastq.gz", "upload_key": "19df9937-3d28-4f0a-b23c-ca50a05cdb0f/4DNFIK5FN5L8.fastq.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/19df9937-3d28-4f0a-b23c-ca50a05cdb0f/4DNFIK5FN5L8.fastq.gz", "tsv_notes": "", "workflow_run_inputs": [{"@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "uuid": "0742a1f7-6143-41a5-a48f-7cf6964d1e61", "display_title": "fastq-first-line v2 run 2021-01-25 23:32:45.594701", "status": "released", "@id": "/workflow-runs-awsem/0742a1f7-6143-41a5-a48f-7cf6964d1e61/", "output_files": [{"workflow_argument_name": "first_line"}], "input_files": [{"workflow_argument_name": "fastq", "value": {"uuid": "19df9937-3d28-4f0a-b23c-ca50a05cdb0f", "display_title": "4DNFIK5FN5L8.fastq.gz", "filename": "LIB034317_TRA00123258_R1.fastq.gz", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIK5FN5L8", "@id": "/files-fastq/4DNFIK5FN5L8/", "status": "released", "file_format": {"file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "display_title": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "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", "status": "released", "uuid": "93a1a931-d55d-4623-adfb-0fa735daf6ae", "@id": "/workflows/4DNWFASTQFO1/", "@type": ["Workflow", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "uuid": "7e60f2a6-a5dd-4a6c-b1ed-e545e076a31a", "display_title": "md5 0.2.6 run 2021-01-24 17:12:37.916720", "status": "released", "@id": "/workflow-runs-awsem/7e60f2a6-a5dd-4a6c-b1ed-e545e076a31a/", "output_files": [{"workflow_argument_name": "report"}], "input_files": [{"workflow_argument_name": "input_file", "value": {"uuid": "19df9937-3d28-4f0a-b23c-ca50a05cdb0f", "display_title": "4DNFIK5FN5L8.fastq.gz", "filename": "LIB034317_TRA00123258_R1.fastq.gz", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIK5FN5L8", "@id": "/files-fastq/4DNFIK5FN5L8/", "status": "released", "file_format": {"file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "display_title": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "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", "status": "released", "uuid": "c77a117b-9a58-477e-aaa5-291a109a99f6", "@id": "/workflows/4DNWF2HFF82B/", "@type": ["Workflow", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "uuid": "a416c73f-a70c-490c-ad9b-fbaff35db53a", "display_title": "fastqc v2 run 2021-01-24 17:12:41.501237", "status": "released", "@id": "/workflow-runs-awsem/a416c73f-a70c-490c-ad9b-fbaff35db53a/", "output_files": [{"workflow_argument_name": "report_zip", "value_qc": {"overall_quality_status": "PASS", "uuid": "13b51a0f-dd5d-4db6-b796-12b05dd47554", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIK5FN5L8/fastqc_report.html", "@id": "/quality-metrics-fastqc/13b51a0f-dd5d-4db6-b796-12b05dd47554/", "display_title": "QualityMetricFastqc from 2021-01-24", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "input_files": [{"workflow_argument_name": "input_fastq", "value": {"uuid": "19df9937-3d28-4f0a-b23c-ca50a05cdb0f", "display_title": "4DNFIK5FN5L8.fastq.gz", "filename": "LIB034317_TRA00123258_R1.fastq.gz", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIK5FN5L8", "@id": "/files-fastq/4DNFIK5FN5L8/", "status": "released", "file_format": {"file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "display_title": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"title": "FastQC v2", "display_title": "FastQC v2 - 4DNWFAEU2GB7", "status": "released", "uuid": "49e96b51-ed6c-4418-a693-d0e9f79adfa5", "@id": "/workflows/4DNWFAEU2GB7/", "@type": ["Workflow", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "uuid": "dbccadc1-7574-4fb8-aed3-e9c09025b37c", "display_title": "rna-strandedness v2 run 2021-01-26 18:02:31.512906", "status": "released", "@id": "/workflow-runs-awsem/dbccadc1-7574-4fb8-aed3-e9c09025b37c/", "output_files": [{"workflow_argument_name": "match_count"}], "input_files": [{"workflow_argument_name": "ACTB_reference", "value": {"uuid": "b59c4b30-52c9-4b30-a455-dfb491df940a", "display_title": "4DNFIAQ4BI8Y.txt", "filename": "ACTB_mouse_reference_21kmer.txt", "@type": ["FileReference", "File", "Item"], "accession": "4DNFIAQ4BI8Y", "@id": "/files-reference/4DNFIAQ4BI8Y/", "status": "released", "file_format": {"file_format": "txt", "uuid": "0cd4e777-a596-4927-95c8-b07716121aa3", "status": "released", "display_title": "txt", "@id": "/file-formats/txt/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "fastq", "value": {"uuid": "19df9937-3d28-4f0a-b23c-ca50a05cdb0f", "display_title": "4DNFIK5FN5L8.fastq.gz", "filename": "LIB034317_TRA00123258_R1.fastq.gz", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIK5FN5L8", "@id": "/files-fastq/4DNFIK5FN5L8/", "status": "released", "file_format": {"file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "display_title": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"title": "Beta-actin gene 21kmer count for RNA-seq data", "display_title": "Beta-actin gene 21kmer count for RNA-seq data - 4DNWFRNASDV1", "status": "released", "uuid": "af97597e-877a-40b7-b211-98ec0cfb17b4", "@id": "/workflows/4DNWFRNASDV1/", "@type": ["Workflow", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "uuid": "3d94bfb2-f35a-4f08-b7a9-c64360c9fbde", "display_title": "encode-rnaseq-stranded 1.1 run 2021-01-27 15:20:36.623474", "status": "released", "@id": "/workflow-runs-awsem/3d94bfb2-f35a-4f08-b7a9-c64360c9fbde/", "output_files": [{"workflow_argument_name": "rna.outbam", "value": {"uuid": "41f2c2e6-eb99-4581-9ade-5715d77b5a7a", "@id": "/files-processed/4DNFIXY52O41/", "display_title": "4DNFIXY52O41.bam", "status": "released", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFIXY52O41", "file_format": {"@id": "/file-formats/bam/", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "file_format": "bam", "display_title": "bam", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "rna.plusbw", "value": {"uuid": "cfbb86e2-5690-441f-bf68-6e79f9a5871f", "@id": "/files-processed/4DNFIY67UHL9/", "display_title": "4DNFIY67UHL9.bw", "status": "released", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFIY67UHL9", "file_format": {"@id": "/file-formats/bw/", "@type": ["FileFormat", "Item"], "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "display_title": "bw", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "rna.minusbw", "value": {"uuid": "9b912a45-03dd-4c46-ba92-a0a0d9434192", "@id": "/files-processed/4DNFIF589CL8/", "display_title": "4DNFIF589CL8.bw", "status": "released", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFIF589CL8", "file_format": {"@id": "/file-formats/bw/", "@type": ["FileFormat", "Item"], "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "display_title": "bw", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "rna.gene_expression", "value": {"uuid": "d186a601-af6b-4c46-967c-845c46f5a007", "@id": "/files-processed/4DNFIYA3FWGJ/", "display_title": "4DNFIYA3FWGJ.tsv", "status": "released", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFIYA3FWGJ", "file_format": {"@id": "/file-formats/tsv/", "@type": ["FileFormat", "Item"], "uuid": "5e8f64b8-6323-410a-8af2-05aba0472f8e", "file_format": "tsv", "display_title": "tsv", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "rna.isoform_expression", "value": {"uuid": "8497276c-3d1c-44a4-a313-c03df4a96fd5", "@id": "/files-processed/4DNFIB518ZH3/", "display_title": "4DNFIB518ZH3.tsv", "status": "released", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFIB518ZH3", "file_format": {"@id": "/file-formats/tsv/", "@type": ["FileFormat", "Item"], "uuid": "5e8f64b8-6323-410a-8af2-05aba0472f8e", "file_format": "tsv", "display_title": "tsv", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "rna.anno_flagstat_qc_json", "value_qc": {"overall_quality_status": "PASS", "uuid": "86096d73-acdb-4227-9d97-38b2404deeb3", "status": "released", "@id": "/quality-metrics-rnaseq/86096d73-acdb-4227-9d97-38b2404deeb3/", "display_title": "QualityMetricRnaseq from 2021-01-27", "@type": ["QualityMetricRnaseq", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "rna.genome_flagstat_qc_json", "value_qc": {"overall_quality_status": "PASS", "uuid": "3f0c6669-a721-4ad8-9a7b-721fa838e84b", "status": "released", "@id": "/quality-metrics-rnaseq/3f0c6669-a721-4ad8-9a7b-721fa838e84b/", "display_title": "QualityMetricRnaseq from 2021-01-27", "@type": ["QualityMetricRnaseq", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "rna.align_log_json", "value_qc": {"overall_quality_status": "PASS", "uuid": "3f0c6669-a721-4ad8-9a7b-721fa838e84b", "status": "released", "@id": "/quality-metrics-rnaseq/3f0c6669-a721-4ad8-9a7b-721fa838e84b/", "display_title": "QualityMetricRnaseq from 2021-01-27", "@type": ["QualityMetricRnaseq", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "rna.qc_json", "value_qc": {"overall_quality_status": "PASS", "uuid": "86096d73-acdb-4227-9d97-38b2404deeb3", "status": "released", "@id": "/quality-metrics-rnaseq/86096d73-acdb-4227-9d97-38b2404deeb3/", "display_title": "QualityMetricRnaseq from 2021-01-27", "@type": ["QualityMetricRnaseq", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "input_files": [{"workflow_argument_name": "rna.align_index", "value": {"uuid": "7ae5a4a4-c53a-4344-ab3f-ebbf487b5efd", "display_title": "4DNFINJIU765.starIndex.tgz", "@type": ["FileReference", "File", "Item"], "accession": "4DNFINJIU765", "@id": "/files-reference/4DNFINJIU765/", "status": "released", "file_format": {"file_format": "starIndex", "uuid": "192d6d3a-6975-4aa5-bcca-38b7dac97ac1", "status": "released", "display_title": "starIndex", "@id": "/file-formats/starIndex/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "rna.chrom_sizes", "value": {"uuid": "be0a9819-d2ce-4422-be4b-234fb1677dd9", "display_title": "4DNFIBP173GC.chrom.sizes", "filename": "mm10_no_alt.chrom.sizes", "@type": ["FileReference", "File", "Item"], "accession": "4DNFIBP173GC", "@id": "/files-reference/4DNFIBP173GC/", "status": "released", "file_format": {"file_format": "chromsizes", "uuid": "d13d06cf-218e-4f61-55f0-93f226248b2c", "status": "released", "display_title": "chromsizes", "@id": "/file-formats/chromsizes/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "rna.fastqs_R1", "value": {"uuid": "663c04f1-992f-426d-8109-1ea5b00925c5", "display_title": "4DNFI5Q5WCMJ.fastq.gz", "filename": "LIB038592_TRA00143595_R1.fastq.gz", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFI5Q5WCMJ", "@id": "/files-fastq/4DNFI5Q5WCMJ/", "status": "released", "file_format": {"file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "display_title": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "rna.fastqs_R1", "value": {"uuid": "19df9937-3d28-4f0a-b23c-ca50a05cdb0f", "display_title": "4DNFIK5FN5L8.fastq.gz", "filename": "LIB034317_TRA00123258_R1.fastq.gz", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIK5FN5L8", "@id": "/files-fastq/4DNFIK5FN5L8/", "status": "released", "file_format": {"file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "display_title": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "rna.fastqs_R2", "value": {"uuid": "e79ea9f6-9dfc-4679-bf20-7da349b0b654", "display_title": "4DNFIY2BQLGL.fastq.gz", "filename": "LIB038592_TRA00143595_R2.fastq.gz", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIY2BQLGL", "@id": "/files-fastq/4DNFIY2BQLGL/", "status": "released", "file_format": {"file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "display_title": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "rna.fastqs_R2", "value": {"uuid": "0f8f4128-82ad-4c6f-b546-0d1f0c99224c", "display_title": "4DNFIXEVQYFN.fastq.gz", "filename": "LIB034317_TRA00123258_R2.fastq.gz", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIXEVQYFN", "@id": "/files-fastq/4DNFIXEVQYFN/", "status": "released", "file_format": {"file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "display_title": "fastq", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "rna.rna_qc_tr_id_to_gene_type_tsv", "value": {"uuid": "fa94b4cb-3d22-4edd-afaa-f2f98bbf9ecc", "display_title": "4DNFINBJ25DT.tsv", "@type": ["FileReference", "File", "Item"], "accession": "4DNFINBJ25DT", "@id": "/files-reference/4DNFINBJ25DT/", "status": "released", "file_format": {"file_format": "tsv", "uuid": "5e8f64b8-6323-410a-8af2-05aba0472f8e", "status": "released", "display_title": "tsv", "@id": "/file-formats/tsv/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "rna.rsem_index", "value": {"uuid": "2995ef5c-4c3f-45d9-bd45-a7b2af4ccb59", "display_title": "4DNFI2GFI8KN.rsemindex.tgz", "@type": ["FileReference", "File", "Item"], "accession": "4DNFI2GFI8KN", "@id": "/files-reference/4DNFI2GFI8KN/", "status": "released", "file_format": {"file_format": "rsemIndex", "uuid": "d444ba45-6cfb-4524-9637-9c55ab39abe4", "status": "released", "display_title": "rsemIndex", "@id": "/file-formats/rsemIndex/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"title": "RNA-seq data processing pipeline, stranded, 1.1", "display_title": "RNA-seq data processing pipeline, stranded, 1.1 - 4DNWFVG24S88", "status": "released", "uuid": "7a7b9e64-05aa-4118-9e65-1a5c21c3fd7f", "@id": "/workflows/4DNWFVG24S88/", "@type": ["Workflow", "Item"], "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": []}