{"lab": {"@id": "/labs/taekjip-ha-lab/", "correspondence": [{"contact_email": "dGFla2ppcEBnbWFpbC5jb20=", "@id": "/users/ea075a00-64b3-44a2-aa60-f0b8e6e72c04/", "display_title": "Taekjip Ha"}], "status": "current", "display_title": "Taekjip Ha, JHU", "title": "Taekjip Ha, JHU", "uuid": "411b90b3-a851-47fb-846e-1eac7be61cb3", "@type": ["Lab", "Item"], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.411b90b3-a851-47fb-846e-1eac7be61cb3"]}}, "award": {"@id": "/awards/1U01DK127432-01/", "description": "RT-CDF: Eukaryotic genomes are packaged in chromatin, linear arrays of nucleosomes in association with nonhistone proteins performing structural, enzymatic, and regulatory functions. This proposal aims to elucidate the interplay between chromatin organization, remodeling and modification and two key nuclear functions: gene transcription and DNA repair, using single molecule imaging in living cells to obtain comprehensive datasets on the real-time dynamics of transcription and DNA repair proteins and chromatin motions, and their integration with theory and modeling with predictive power.  We will apply single molecule tracking (SMT) to image at high spatiotemporal resolution the organization, dynamics, regulation and function of a prototypical pioneer transcription factor, GAGA factor (GAF) in Drosophila. We will image the global and local nuclear organization and dynamics of wild-type and mutant GAF binding to cognate DNA elements genome-wide, and at Hsp70 promoters in live hemocytes. We will image the global and local dynamics of eight prominent chromatin and transcription protein effectors linked to GAF functions. SMT datasets from the factors imaged above are used to construct theoretical models for GAF interactions with chromatin targets and test models by experimental manipulation. Studies will be extended to human NF-Y, a distinct pioneer factor that makes accessible chromatin at the Hsp70 promoter in human cells.  We will examine the interplay between chromatin organization and dynamics and DNA repair, using very fast (vf) CRISPR that can generate a double strand break (DSB) anywhere in the genome with high spatiotemporal resolution. We will determine DSB repair kinetics and chromatin reorganization through time- resolved chromatin analysis and real-time imaging of repair factors after generating DSB. We will determine the impact of topologically associated domains and loop extrusion on chromatin modifications and relaxations that accompany DNA repair, and integrate chromatin and DNA repair kinetics datasets to construct theoretical models for 4D chromatin reorganization during DSB repair. We will employ a series of chromatin remodeler and DNA damage response mutants to document causal relationships, and expand the reach of vfCRISPR to other DNA repair processes including base excision repair and mismatch repair.  We will merge the above approaches to explore how DNA repair-mediated chromatin alterations affect transcription in human cells, and reciprocally, how transcription and associated chromatin changes influence DNA repair dynamics. We will image dynamics of pioneer and non-pioneer factors and key DNA repair enzymes at the active Hsp70 gene in living human cells, varying the timing of DSB and heat shock to evaluate the influence of DSB on different stages of transcription. Simultaneous imaging of labeled locus and nascent Hsp70 mRNA will reveal how transcription affects dynamics of the damaged locus.", "name": "1U01DK127432-01", "project": "4DN", "display_title": "CHROMATIN FUNCTION DURING TRANSCRIPTION AND DNA REPAIR AT SINGLE MOLECULE RESOLUTION IN LIVING CELLS", "uuid": "b9ff5f2d-68aa-4a4b-9c3d-54707e1798ec", "center_title": "Ha", "status": "current", "@type": ["Award", "Item"], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "aliases": ["taekjip-ha-lab:atac-seq-hek293-1h-pcRNA"], "accession": "4DNESRIVHLUJ", "condition": "photocleavable mgRNA - 1 h post light", "description": "ATAC-seq on HEK293 cells - 1h after light Cas9-AluGG pcRNA (light-deactivatable CRISPR)", "date_created": "2022-02-14T03:09:53.415566+00:00", "submitted_by": {"error": "no view permissions"}, "dataset_label": "ATAC-Seq on HEK293 cells after multi-target Crispr", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2023-08-18T18:46:05.256856+00:00"}, "public_release": "2022-03-14", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"@id": "/experiments-atacseq/4DNEX8SG7PVA/", "status": "released", "@type": ["ExperimentAtacseq", "Experiment", "Item"], "uuid": "53bd0759-8a99-4075-9e68-100b4521eb4d", "accession": "4DNEX8SG7PVA", "display_title": "ATAC-seq on HEK293 (Tier 2) - 4DNEX8SG7PVA", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 2, "tec_rep_no": 1, "replicate_exp": {"@id": "/experiments-atacseq/4DNEXABQPDBS/", "status": "released", "@type": ["ExperimentAtacseq", "Experiment", "Item"], "uuid": "13c5dc94-948e-4bd5-af7e-050357c3e5a9", "accession": "4DNEXABQPDBS", "display_title": "ATAC-seq on HEK293 (Tier 2) - 4DNEXABQPDBS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "static_content": [{"content": {"name": "9db52e0e-2e81-42fb-9966-b0de17400f02", "award": {"@type": ["Award", "Item"], "display_title": "CHROMATIN FUNCTION DURING TRANSCRIPTION AND DNA REPAIR AT SINGLE MOLECULE RESOLUTION IN LIVING CELLS", "status": "current", "uuid": "b9ff5f2d-68aa-4a4b-9c3d-54707e1798ec", "@id": "/awards/1U01DK127432-01/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "display_title": "4DNESRIVHLUJ - Processed files", "uuid": "9db52e0e-2e81-42fb-9966-b0de17400f02", "lab": {"display_title": "Taekjip Ha, JHU", "uuid": "411b90b3-a851-47fb-846e-1eac7be61cb3", "@type": ["Lab", "Item"], "@id": "/labs/taekjip-ha-lab/", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.411b90b3-a851-47fb-846e-1eac7be61cb3"]}}, "@id": "/higlass-view-configs/9db52e0e-2e81-42fb-9966-b0de17400f02/", "@type": ["HiglassViewConfig", "UserContent", "Item"], "filetype": "HiglassViewConfig", "title": "4DNESRIVHLUJ - Processed files", "status": "released", "description": "4DNESRIVHLUJ (ATAC-seq on HEK293 cells - 1h after light Cas9-AluGG pcRNA (light-deactivatable CRISPR)): 4DNFIDL1QBTI, 4DNFID7VD3ZM, 4DNFIB5PL85Q", "contributing_labs": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}, "location": "tab:processed-files", "description": "auto_generated_higlass_view_config"}], "processed_files": [{"higlass_uid": "2d0ada3d-c900-4cd4-b982-4acbf0b6a356", "file_type": "peaks", "@type": ["FileProcessed", "File", "Item"], "upload_key": "10e6b232-150c-4647-89a2-bdcd4dd3770d/4DNFIDL1QBTI.bb", "md5sum": "0337533f079d4be44f289b6de428242c", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/10e6b232-150c-4647-89a2-bdcd4dd3770d/4DNFIDL1QBTI.bb", "uuid": "10e6b232-150c-4647-89a2-bdcd4dd3770d", "file_type_detailed": "peaks (bigbed)", "genome_assembly": "GRCh38", "status": "released", "file_classification": "processed file", "accession": "4DNFIDL1QBTI", "file_format": {"status": "released", "display_title": "bigbed", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bigbed/", "uuid": "bbafb7f8-98d5-48d7-8e75-dc40a5186e19", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "display_title": "4DNFIDL1QBTI.bb", "file_size": 10219148, "@id": "/files-processed/4DNFIDL1QBTI/", "href": "/files-processed/4DNFIDL1QBTI/@@download/4DNFIDL1QBTI.bb", "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"status": "released", "@type": ["HiglassViewConfig", "UserContent", "Item"], "uuid": "c32ee169-0d32-4cc8-8a31-6fba5503ee2f", "display_title": "4DNFIDL1QBTI - peaks for HEK293 (Tier 2) ATAC-seq", "@id": "/higlass-view-configs/c32ee169-0d32-4cc8-8a31-6fba5503ee2f/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "quality_metric": {"display_title": "QualityMetricAtacseq from 2022-02-25", "uuid": "6c52b94c-7058-42cd-9598-1d468bdf8188", "@id": "/quality-metrics-atacseq/6c52b94c-7058-42cd-9598-1d468bdf8188/", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIDL1QBTI/qc_report.html", "@type": ["QualityMetricAtacseq", "QualityMetric", "Item"], "overall_quality_status": "PASS", "status": "released", "quality_metric_summary": [{"title": "Optimal Peaks", "value": "211833", "numberType": "integer"}, {"title": "Rescue Ratio", "tooltip": "Ratio of number of peaks (Nt) relative to peak calling based on psuedoreplicates (Np) [max(Np,Nt) / min (Np,Nt)]", "value": "1.01", "numberType": "float"}, {"title": "Self Consistency Ratio", "tooltip": "Ratio of number of peaks in two replicates [max(N1,N2) / min (N1,N2)]", "value": "1.07", "numberType": "float"}, {"title": "Fraction of Reads in Peaks", "value": "0.28", "numberType": "float"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "name": "4dn-dcic-lab", "@id": "/labs/4dn-dcic-lab/", "display_title": "4DN DCIC, HMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "contributing_labs": [{"name": "taekjip-ha-lab", "uuid": "411b90b3-a851-47fb-846e-1eac7be61cb3", "@id": "/labs/taekjip-ha-lab/", "status": "current", "@type": ["Lab", "Item"], "display_title": "Taekjip Ha, JHU", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.411b90b3-a851-47fb-846e-1eac7be61cb3"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"dataset": "ATAC-Seq on HEK293 cells after multi-target Crispr", "condition": "photocleavable mgRNA - 1 h post light", "experimental_lab": "Taekjip Ha, JHU", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "ATAC-seq", "biosource_name": "HEK293 (Tier 2)", "lab_name": "4DN DCIC, HMS", "track_title": "peaks for HEK293 (Tier 2) ATAC-seq"}, "external_references": [], "last_modified": {"date_modified": "2022-05-03T21:46:27.491394+00:00"}}, {"higlass_uid": "729ce8aa-e65a-47f6-8ae0-e5daa2d38c73", "file_type": "conservative peaks", "@type": ["FileProcessed", "File", "Item"], "upload_key": "b38790fc-3b1f-475c-b7db-27d0ddac4ebe/4DNFID7VD3ZM.bb", "md5sum": "2df2d3ac375e7dbd4a118f23916e1ef5", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/b38790fc-3b1f-475c-b7db-27d0ddac4ebe/4DNFID7VD3ZM.bb", "uuid": "b38790fc-3b1f-475c-b7db-27d0ddac4ebe", "file_type_detailed": "conservative peaks (bigbed)", "genome_assembly": "GRCh38", "status": "released", "file_classification": "processed file", "accession": "4DNFID7VD3ZM", "file_format": {"status": "released", "display_title": "bigbed", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bigbed/", "uuid": "bbafb7f8-98d5-48d7-8e75-dc40a5186e19", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "display_title": "4DNFID7VD3ZM.bb", "file_size": 10159937, "@id": "/files-processed/4DNFID7VD3ZM/", "href": "/files-processed/4DNFID7VD3ZM/@@download/4DNFID7VD3ZM.bb", "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"status": "released", "@type": ["HiglassViewConfig", "UserContent", "Item"], "uuid": "328ec426-e772-4fe5-9ea9-2950c5eb18d7", "display_title": "4DNFID7VD3ZM - conservative peaks for HEK293 (Tier 2) ATAC-seq", "@id": "/higlass-view-configs/328ec426-e772-4fe5-9ea9-2950c5eb18d7/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "lab": {"status": "current", "@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "name": "4dn-dcic-lab", "@id": "/labs/4dn-dcic-lab/", "display_title": "4DN DCIC, HMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "contributing_labs": [{"name": "taekjip-ha-lab", "uuid": "411b90b3-a851-47fb-846e-1eac7be61cb3", "@id": "/labs/taekjip-ha-lab/", "status": "current", "@type": ["Lab", "Item"], "display_title": "Taekjip Ha, JHU", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.411b90b3-a851-47fb-846e-1eac7be61cb3"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"dataset": "ATAC-Seq on HEK293 cells after multi-target Crispr", "condition": "photocleavable mgRNA - 1 h post light", "experimental_lab": "Taekjip Ha, JHU", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "ATAC-seq", "biosource_name": "HEK293 (Tier 2)", "lab_name": "4DN DCIC, HMS", "track_title": "conservative peaks for HEK293 (Tier 2) ATAC-seq"}, "external_references": [], "last_modified": {"date_modified": "2022-05-03T21:46:25.458113+00:00"}}, {"higlass_uid": "0572a2c7-35fd-4f9f-8fee-c732f864791a", "file_type": "signal fold change", "@type": ["FileProcessed", "File", "Item"], "upload_key": "2932a9a7-7018-4ef8-9d60-21d0ab8f37eb/4DNFIB5PL85Q.bw", "md5sum": "293010b9f726a04802d6511b8339de6d", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/2932a9a7-7018-4ef8-9d60-21d0ab8f37eb/4DNFIB5PL85Q.bw", "uuid": "2932a9a7-7018-4ef8-9d60-21d0ab8f37eb", "file_type_detailed": "signal fold change (bw)", "genome_assembly": "GRCh38", "status": "released", "file_classification": "processed file", "accession": "4DNFIB5PL85Q", "file_format": {"status": "released", "display_title": "bw", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bw/", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "display_title": "4DNFIB5PL85Q.bw", "file_size": 2265976890, "@id": "/files-processed/4DNFIB5PL85Q/", "href": "/files-processed/4DNFIB5PL85Q/@@download/4DNFIB5PL85Q.bw", "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"status": "released", "@type": ["HiglassViewConfig", "UserContent", "Item"], "uuid": "71249a1d-c8b4-4a2a-8f16-046443cafb7b", "display_title": "4DNFIB5PL85Q - signal fold change for HEK293 (Tier 2) ATAC-seq", "@id": "/higlass-view-configs/71249a1d-c8b4-4a2a-8f16-046443cafb7b/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "lab": {"status": "current", "@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "name": "4dn-dcic-lab", "@id": "/labs/4dn-dcic-lab/", "display_title": "4DN DCIC, HMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "contributing_labs": [{"name": "taekjip-ha-lab", "uuid": "411b90b3-a851-47fb-846e-1eac7be61cb3", "@id": "/labs/taekjip-ha-lab/", "status": "current", "@type": ["Lab", "Item"], "display_title": "Taekjip Ha, JHU", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.411b90b3-a851-47fb-846e-1eac7be61cb3"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"dataset": "ATAC-Seq on HEK293 cells after multi-target Crispr", "condition": "photocleavable mgRNA - 1 h post light", "experimental_lab": "Taekjip Ha, JHU", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "ATAC-seq", "biosource_name": "HEK293 (Tier 2)", "lab_name": "4DN DCIC, HMS", "track_title": "signal fold change for HEK293 (Tier 2) ATAC-seq"}, "external_references": [], "last_modified": {"date_modified": "2022-05-03T21:46:23.553892+00:00"}}], "project_release": "2022-03-14", "experiments_in_set": [{"status": "released", "@type": ["ExperimentAtacseq", "Experiment", "Item"], "files": [{"accession": "4DNFIFXEKGWR", "md5sum": "0e8fce84ad2db10c9c9daaf2ec7f90e0", "file_classification": "raw file", "upload_key": "ed0caa91-3649-4547-b26b-26287e0779f8/4DNFIFXEKGWR.fastq.gz", "display_title": "4DNFIFXEKGWR.fastq.gz", "uuid": "ed0caa91-3649-4547-b26b-26287e0779f8", "@id": "/files-fastq/4DNFIFXEKGWR/", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/ed0caa91-3649-4547-b26b-26287e0779f8/4DNFIFXEKGWR.fastq.gz", "file_type": "reads", "href": "/files-fastq/4DNFIFXEKGWR/@@download/4DNFIFXEKGWR.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "paired_end": "1", "file_size": 2227337409, "file_type_detailed": "reads (fastq)", "lab": {"name": "taekjip-ha-lab", "@type": ["Lab", "Item"], "@id": "/labs/taekjip-ha-lab/", "display_title": "Taekjip Ha, JHU", "status": "current", "uuid": "411b90b3-a851-47fb-846e-1eac7be61cb3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.411b90b3-a851-47fb-846e-1eac7be61cb3"]}}, "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIFXEKGWR/fastqc_report.html", "Total Sequences": 70999609, "status": "released", "overall_quality_status": "PASS", "Sequence length": "50", "uuid": "0d6c51da-ceff-4387-8ea7-d5aa9ef4077c", "display_title": "QualityMetricFastqc from 2022-02-23", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/0d6c51da-ceff-4387-8ea7-d5aa9ef4077c/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"uuid": "d3631a5d-ffed-4887-844a-9a3a4057fd7d", "file_type_detailed": "reads (fastq)", "display_title": "4DNFIKGZ7HVI.fastq.gz", "accession": "4DNFIKGZ7HVI", "paired_end": "2", "status": "released", "@id": "/files-fastq/4DNFIKGZ7HVI/", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "file_format": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "track_and_facet_info": {"experimental_lab": "Taekjip Ha, JHU", "experiment_type": "ATAC-seq", "experiment_bucket": "raw file", "dataset": "ATAC-Seq on HEK293 cells after multi-target Crispr", "condition": "photocleavable mgRNA - 1 h post light", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HEK293 (Tier 2)", "lab_name": "Taekjip Ha, JHU"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"accession": "4DNFIKGZ7HVI", "md5sum": "7a2ac1e76817024fba49f7440f0bb051", "file_classification": "raw file", "upload_key": "d3631a5d-ffed-4887-844a-9a3a4057fd7d/4DNFIKGZ7HVI.fastq.gz", "display_title": "4DNFIKGZ7HVI.fastq.gz", "uuid": "d3631a5d-ffed-4887-844a-9a3a4057fd7d", "@id": "/files-fastq/4DNFIKGZ7HVI/", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/d3631a5d-ffed-4887-844a-9a3a4057fd7d/4DNFIKGZ7HVI.fastq.gz", "file_type": "reads", "href": "/files-fastq/4DNFIKGZ7HVI/@@download/4DNFIKGZ7HVI.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "paired_end": "2", "file_size": 2299202743, "file_type_detailed": "reads (fastq)", "lab": {"name": "taekjip-ha-lab", "@type": ["Lab", "Item"], "@id": "/labs/taekjip-ha-lab/", "display_title": "Taekjip Ha, JHU", "status": "current", "uuid": "411b90b3-a851-47fb-846e-1eac7be61cb3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.411b90b3-a851-47fb-846e-1eac7be61cb3"]}}, "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIKGZ7HVI/fastqc_report.html", "Total Sequences": 70999609, "status": "released", "overall_quality_status": "PASS", "Sequence length": "50", "uuid": "32100342-07fe-48fb-9ee6-e1f53de7a667", "display_title": "QualityMetricFastqc from 2022-02-23", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/32100342-07fe-48fb-9ee6-e1f53de7a667/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"uuid": "ed0caa91-3649-4547-b26b-26287e0779f8", "file_type_detailed": "reads (fastq)", "display_title": "4DNFIFXEKGWR.fastq.gz", "accession": "4DNFIFXEKGWR", "paired_end": "1", "status": "released", "@id": "/files-fastq/4DNFIFXEKGWR/", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "file_format": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "track_and_facet_info": {"experimental_lab": "Taekjip Ha, JHU", "experiment_type": "ATAC-seq", "experiment_bucket": "raw file", "dataset": "ATAC-Seq on HEK293 cells after multi-target Crispr", "condition": "photocleavable mgRNA - 1 h post light", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HEK293 (Tier 2)", "lab_name": "Taekjip Ha, JHU"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "accession": "4DNEX8SG7PVA", "display_title": "ATAC-seq on HEK293 (Tier 2) - 4DNEX8SG7PVA", "uuid": "53bd0759-8a99-4075-9e68-100b4521eb4d", "@id": "/experiments-atacseq/4DNEX8SG7PVA/", "processed_files": [{"href": "/files-processed/4DNFIBXM1SZU/@@download/4DNFIBXM1SZU.bed.gz", "md5sum": "6901dd3a2643b04c654e097ba018e966", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/acd3e716-7fac-44e0-96d6-cde70e146a5f/4DNFIBXM1SZU.bed.gz", "file_format": {"display_title": "bed", "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "status": "released", "@id": "/file-formats/bed/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_classification": "processed file", "upload_key": "acd3e716-7fac-44e0-96d6-cde70e146a5f/4DNFIBXM1SZU.bed.gz", "file_type_detailed": "read positions (bed)", "file_size": 878124898, "@type": ["FileProcessed", "File", "Item"], "status": "released", "display_title": "4DNFIBXM1SZU.bed.gz", "@id": "/files-processed/4DNFIBXM1SZU/", "accession": "4DNFIBXM1SZU", "uuid": "acd3e716-7fac-44e0-96d6-cde70e146a5f", "genome_assembly": "GRCh38", "file_type": "read positions", "quality_metric": {"status": "released", "@id": "/quality-metrics-atacseq/0176f11c-258f-46c7-94e2-f487729a66bf/", "overall_quality_status": "PASS", "uuid": "0176f11c-258f-46c7-94e2-f487729a66bf", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIBXM1SZU/qc_report.html", "@type": ["QualityMetricAtacseq", "QualityMetric", "Item"], "display_title": "QualityMetricAtacseq from 2022-02-25", "quality_metric_summary": [{"title": "Percent mitochondrial reads", "value": "7.05", "numberType": "percent"}, {"title": "Nonredundant Read Fraction (NRF)", "value": "0.94", "tooltip": "distinct non-mito read pairs / total non-mito read pairs", "numberType": "float"}, {"title": "PCR Bottleneck Coefficient (PBC)", "value": "0.95", "tooltip": "one-read non-mito read pairs / distinct non-mito read pairs", "numberType": "float"}, {"title": "Filtered & Deduped Reads", "value": "52367963", "numberType": "integer"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2022-05-03T21:12:51.765040+00:00"}, "lab": {"display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "status": "current", "name": "4dn-dcic-lab", "@id": "/labs/4dn-dcic-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "contributing_labs": [{"uuid": "411b90b3-a851-47fb-846e-1eac7be61cb3", "name": "taekjip-ha-lab", "@type": ["Lab", "Item"], "display_title": "Taekjip Ha, JHU", "status": "current", "@id": "/labs/taekjip-ha-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.411b90b3-a851-47fb-846e-1eac7be61cb3"]}}], "external_references": [], "track_and_facet_info": {"experimental_lab": "Taekjip Ha, JHU", "experiment_type": "ATAC-seq", "experiment_bucket": "processed file", "dataset": "ATAC-Seq on HEK293 cells after multi-target Crispr", "condition": "photocleavable mgRNA - 1 h post light", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HEK293 (Tier 2)", "lab_name": "4DN DCIC, HMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "biosample": {"accession": "4DNBS86B5OZD", "biosource_summary": "HEK293 (Tier 2)", "uuid": "5eab48af-3e55-4770-a6e0-6ae2d46d2095", "status": "released", "@id": "/biosamples/4DNBS86B5OZD/", "treatments_summary": "Transient transfection of AluGG-pcRNA and Light (1.0h)", "@type": ["Biosample", "Item"], "biosample_type": "immortalized cells", "biosample_category": ["Tier 2"], "display_title": "4DNBS86B5OZD", "modifications_summary": "None", "tissue_organ_info": {"tissue_source": "kidney", "organ_system": ["kidney", "renal system"]}, "biosource": [{"uuid": "d1586f88-0fdf-42dd-bfd3-953bdef7b76e", "accession": "4DNSRVF4XB1F", "@type": ["Biosource", "Item"], "biosource_type": "immortalized cell line", "display_title": "HEK293 (Tier 2) - 4DNSRVF4XB1F", "@id": "/biosources/4DNSRVF4XB1F/", "status": "released", "cell_line_tier": "Tier 2", "cell_line": {"synonyms": ["human embryonic kidney cell"], "uuid": "0074518c-23ed-409a-965c-ad76188e5d83", "preferred_name": "HEK293", "@id": "/ontology-terms/EFO:0001182/", "@type": ["OntologyTerm", "Item"], "status": "released", "term_name": "HEK293", "term_id": "EFO:0001182", "display_title": "HEK293", "slim_terms": [{"@id": "/ontology-terms/GO:0005623/", "status": "current", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/CL:0000000/", "status": "released", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"@type": ["OntologyTerm", "Item"], "preferred_name": "kidney", "uuid": "111167bc-8535-4448-903e-854af460a233", "status": "released", "@id": "/ontology-terms/UBERON:0002113/", "term_name": "kidney", "display_title": "kidney", "synonyms": ["reniculate kidney"], "term_id": "UBERON:0002113", "slim_terms": [{"uuid": "111167bc-8535-4448-903e-854af460a233", "status": "released", "@id": "/ontology-terms/UBERON:0002113/", "@type": ["OntologyTerm", "Item"], "display_title": "kidney", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "111130bc-8535-4448-903e-854af460a233", "status": "released", "@id": "/ontology-terms/UBERON:0001008/", "@type": ["OntologyTerm", "Item"], "display_title": "renal system", "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": {"scientific_name": "Homo sapiens", "@type": ["Organism", "Item"], "name": "human", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "@id": "/organisms/9606/", "status": "released", "display_title": "H. sapiens", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "treatments": [{"biological_agent": "Cas9-gRNA RNP with photocleavable AluGG-pcRNA", "display_title": "Transient transfection of AluGG-pcRNA", "@type": ["TreatmentAgent", "Treatment", "Item"], "@id": "/treatments-agent/3803519f-d505-4aef-82c3-5cfd2178c30b/", "uuid": "3803519f-d505-4aef-82c3-5cfd2178c30b", "status": "released", "treatment_type": "Transient Transfection", "description": "Electroporation of preassembled Cas9-gRNA RNP using a light deactivatable photocleavable AluGG-pcRNA", "constructs": [{"uuid": "55af3fe7-9c8b-412a-80c1-ccf79dbbda74", "name": "AluGG-pcRNA", "display_title": "AluGG-pcRNA", "@type": ["Construct", "Item"], "@id": "/constructs/55af3fe7-9c8b-412a-80c1-ccf79dbbda74/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "Light (1.0h)", "duration": 1.0, "@type": ["TreatmentAgent", "Treatment", "Item"], "@id": "/treatments-agent/33573727-88d8-40ad-a4c6-b2e27b111771/", "duration_units": "hour", "uuid": "33573727-88d8-40ad-a4c6-b2e27b111771", "status": "released", "treatment_type": "Light", "description": "1 hour light exposure", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "cell_culture_details": [{"uuid": "597300a8-adef-4cbe-b55a-3d8b0a45dc3a", "status": "released", "@id": "/biosample-cell-cultures/597300a8-adef-4cbe-b55a-3d8b0a45dc3a/", "in_vitro_differentiated": "No", "display_title": "BiosampleCellCulture from 2022-02-14", "@type": ["BiosampleCellCulture", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "badges": [{"messages": ["Biosample missing morphology_image"], "badge": {"badge_icon": "/static/img/badges/biosample-icon.svg", "title": "Biosample Metadata Incomplete", "display_title": "Biosample Metadata Incomplete", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "@type": ["Badge", "Item"], "warning": "Biosample Metadata Incomplete", "badge_classification": "Warning", "status": "released", "@id": "/badges/biosample-metadata-incomplete/", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_type": {"uuid": "5b35245d-5777-4983-b7e8-8dffd9ab83ab", "status": "released", "assay_subclass_short": "Open Chromatin", "assay_subclassification": "Open Chromatin", "title": "ATAC-seq", "@type": ["ExperimentType", "Item"], "experiment_category": "Sequencing", "display_title": "ATAC-seq", "assay_classification": "Linear DNA Enrichment", "@id": "/experiment-types/atac-seq/", "other_tags": ["1D"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "experiment_categorizer": {"field": "Default"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2022-03-14T16:16:46.452994+00:00"}}, {"status": "released", "@type": ["ExperimentAtacseq", "Experiment", "Item"], "files": [{"accession": "4DNFI1LKL4D9", "md5sum": "6fc3aa382b5fde9327f2052f0358d001", "file_classification": "raw file", "upload_key": "b24979de-f510-4ea7-9366-ac09e93d2c27/4DNFI1LKL4D9.fastq.gz", "display_title": "4DNFI1LKL4D9.fastq.gz", "uuid": "b24979de-f510-4ea7-9366-ac09e93d2c27", "@id": "/files-fastq/4DNFI1LKL4D9/", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/b24979de-f510-4ea7-9366-ac09e93d2c27/4DNFI1LKL4D9.fastq.gz", "file_type": "reads", "href": "/files-fastq/4DNFI1LKL4D9/@@download/4DNFI1LKL4D9.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "paired_end": "1", "file_size": 2905124558, "file_type_detailed": "reads (fastq)", "lab": {"name": "taekjip-ha-lab", "@type": ["Lab", "Item"], "@id": "/labs/taekjip-ha-lab/", "display_title": "Taekjip Ha, JHU", "status": "current", "uuid": "411b90b3-a851-47fb-846e-1eac7be61cb3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.411b90b3-a851-47fb-846e-1eac7be61cb3"]}}, "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI1LKL4D9/fastqc_report.html", "Total Sequences": 90206741, "status": "released", "overall_quality_status": "PASS", "Sequence length": "50", "uuid": "6a77ac6a-08d7-4679-a082-2b69d59a9976", "display_title": "QualityMetricFastqc from 2022-02-23", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/6a77ac6a-08d7-4679-a082-2b69d59a9976/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"uuid": "99feab82-80fc-4377-a3a3-212fab5dd088", "file_type_detailed": "reads (fastq)", "display_title": "4DNFICUJU7GO.fastq.gz", "accession": "4DNFICUJU7GO", "paired_end": "2", "status": "released", "@id": "/files-fastq/4DNFICUJU7GO/", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "file_format": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "track_and_facet_info": {"experimental_lab": "Taekjip Ha, JHU", "experiment_type": "ATAC-seq", "experiment_bucket": "raw file", "dataset": "ATAC-Seq on HEK293 cells after multi-target Crispr", "condition": "photocleavable mgRNA - 1 h post light", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HEK293 (Tier 2)", "lab_name": "Taekjip Ha, JHU"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"accession": "4DNFICUJU7GO", "md5sum": "f1b7e1818adfe611a6040e7a709782c2", "file_classification": "raw file", "upload_key": "99feab82-80fc-4377-a3a3-212fab5dd088/4DNFICUJU7GO.fastq.gz", "display_title": "4DNFICUJU7GO.fastq.gz", "uuid": "99feab82-80fc-4377-a3a3-212fab5dd088", "@id": "/files-fastq/4DNFICUJU7GO/", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/99feab82-80fc-4377-a3a3-212fab5dd088/4DNFICUJU7GO.fastq.gz", "file_type": "reads", "href": "/files-fastq/4DNFICUJU7GO/@@download/4DNFICUJU7GO.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "paired_end": "2", "file_size": 2837294738, "file_type_detailed": "reads (fastq)", "lab": {"name": "taekjip-ha-lab", "@type": ["Lab", "Item"], "@id": "/labs/taekjip-ha-lab/", "display_title": "Taekjip Ha, JHU", "status": "current", "uuid": "411b90b3-a851-47fb-846e-1eac7be61cb3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.411b90b3-a851-47fb-846e-1eac7be61cb3"]}}, "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFICUJU7GO/fastqc_report.html", "Total Sequences": 90206741, "status": "released", "overall_quality_status": "PASS", "Sequence length": "50", "uuid": "269c831e-a4ff-471d-8b82-7a4d1d6c59bf", "display_title": "QualityMetricFastqc from 2022-02-23", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/269c831e-a4ff-471d-8b82-7a4d1d6c59bf/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"uuid": "b24979de-f510-4ea7-9366-ac09e93d2c27", "file_type_detailed": "reads (fastq)", "display_title": "4DNFI1LKL4D9.fastq.gz", "accession": "4DNFI1LKL4D9", "paired_end": "1", "status": "released", "@id": "/files-fastq/4DNFI1LKL4D9/", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "file_format": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "track_and_facet_info": {"experimental_lab": "Taekjip Ha, JHU", "experiment_type": "ATAC-seq", "experiment_bucket": "raw file", "dataset": "ATAC-Seq on HEK293 cells after multi-target Crispr", "condition": "photocleavable mgRNA - 1 h post light", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HEK293 (Tier 2)", "lab_name": "Taekjip Ha, JHU"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "accession": "4DNEXABQPDBS", "display_title": "ATAC-seq on HEK293 (Tier 2) - 4DNEXABQPDBS", "uuid": "13c5dc94-948e-4bd5-af7e-050357c3e5a9", "@id": "/experiments-atacseq/4DNEXABQPDBS/", "processed_files": [{"href": "/files-processed/4DNFIRA9IK9P/@@download/4DNFIRA9IK9P.bed.gz", "md5sum": "2f2ab270928cb0cfb1ea4253b86f2788", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/ff6030d6-1154-496a-9be3-dbae9d5ba590/4DNFIRA9IK9P.bed.gz", "file_format": {"display_title": "bed", "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "status": "released", "@id": "/file-formats/bed/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_classification": "processed file", "upload_key": "ff6030d6-1154-496a-9be3-dbae9d5ba590/4DNFIRA9IK9P.bed.gz", "file_type_detailed": "read positions (bed)", "file_size": 1029377687, "@type": ["FileProcessed", "File", "Item"], "status": "released", "display_title": "4DNFIRA9IK9P.bed.gz", "@id": "/files-processed/4DNFIRA9IK9P/", "accession": "4DNFIRA9IK9P", "uuid": "ff6030d6-1154-496a-9be3-dbae9d5ba590", "genome_assembly": "GRCh38", "file_type": "read positions", "quality_metric": {"status": "released", "@id": "/quality-metrics-atacseq/819ba661-3e4f-4ed5-a9a3-29a914be0178/", "overall_quality_status": "PASS", "uuid": "819ba661-3e4f-4ed5-a9a3-29a914be0178", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIRA9IK9P/qc_report.html", "@type": ["QualityMetricAtacseq", "QualityMetric", "Item"], "display_title": "QualityMetricAtacseq from 2022-02-25", "quality_metric_summary": [{"title": "Percent mitochondrial reads", "value": "11.94", "numberType": "percent"}, {"title": "Nonredundant Read Fraction (NRF)", "value": "0.93", "tooltip": "distinct non-mito read pairs / total non-mito read pairs", "numberType": "float"}, {"title": "PCR Bottleneck Coefficient (PBC)", "value": "0.94", "tooltip": "one-read non-mito read pairs / distinct non-mito read pairs", "numberType": "float"}, {"title": "Filtered & Deduped Reads", "value": "61423056", "numberType": "integer"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2022-05-03T21:12:44.799048+00:00"}, "lab": {"display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "status": "current", "name": "4dn-dcic-lab", "@id": "/labs/4dn-dcic-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "contributing_labs": [{"uuid": "411b90b3-a851-47fb-846e-1eac7be61cb3", "name": "taekjip-ha-lab", "@type": ["Lab", "Item"], "display_title": "Taekjip Ha, JHU", "status": "current", "@id": "/labs/taekjip-ha-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.411b90b3-a851-47fb-846e-1eac7be61cb3"]}}], "external_references": [], "track_and_facet_info": {"experimental_lab": "Taekjip Ha, JHU", "experiment_type": "ATAC-seq", "experiment_bucket": "processed file", "dataset": "ATAC-Seq on HEK293 cells after multi-target Crispr", "condition": "photocleavable mgRNA - 1 h post light", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HEK293 (Tier 2)", "lab_name": "4DN DCIC, HMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "biosample": {"accession": "4DNBSEPLZJ1Y", "biosource_summary": "HEK293 (Tier 2)", "uuid": "2758ec20-035f-4068-9ed6-71e3b6f4109c", "status": "released", "@id": "/biosamples/4DNBSEPLZJ1Y/", "treatments_summary": "Transient transfection of AluGG-pcRNA and Light (1.0h)", "@type": ["Biosample", "Item"], "biosample_type": "immortalized cells", "biosample_category": ["Tier 2"], "display_title": "4DNBSEPLZJ1Y", "modifications_summary": "None", "tissue_organ_info": {"tissue_source": "kidney", "organ_system": ["kidney", "renal system"]}, "biosource": [{"uuid": "d1586f88-0fdf-42dd-bfd3-953bdef7b76e", "accession": "4DNSRVF4XB1F", "@type": ["Biosource", "Item"], "biosource_type": "immortalized cell line", "display_title": "HEK293 (Tier 2) - 4DNSRVF4XB1F", "@id": "/biosources/4DNSRVF4XB1F/", "status": "released", "cell_line_tier": "Tier 2", "cell_line": {"synonyms": ["human embryonic kidney cell"], "uuid": "0074518c-23ed-409a-965c-ad76188e5d83", "preferred_name": "HEK293", "@id": "/ontology-terms/EFO:0001182/", "@type": ["OntologyTerm", "Item"], "status": "released", "term_name": "HEK293", "term_id": "EFO:0001182", "display_title": "HEK293", "slim_terms": [{"@id": "/ontology-terms/GO:0005623/", "status": "current", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/CL:0000000/", "status": "released", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"@type": ["OntologyTerm", "Item"], "preferred_name": "kidney", "uuid": "111167bc-8535-4448-903e-854af460a233", "status": "released", "@id": "/ontology-terms/UBERON:0002113/", "term_name": "kidney", "display_title": "kidney", "synonyms": ["reniculate kidney"], "term_id": "UBERON:0002113", "slim_terms": [{"uuid": "111167bc-8535-4448-903e-854af460a233", "status": "released", "@id": "/ontology-terms/UBERON:0002113/", "@type": ["OntologyTerm", "Item"], "display_title": "kidney", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "111130bc-8535-4448-903e-854af460a233", "status": "released", "@id": "/ontology-terms/UBERON:0001008/", "@type": ["OntologyTerm", "Item"], "display_title": "renal system", "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": {"scientific_name": "Homo sapiens", "@type": ["Organism", "Item"], "name": "human", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "@id": "/organisms/9606/", "status": "released", "display_title": "H. sapiens", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "treatments": [{"biological_agent": "Cas9-gRNA RNP with photocleavable AluGG-pcRNA", "display_title": "Transient transfection of AluGG-pcRNA", "@type": ["TreatmentAgent", "Treatment", "Item"], "@id": "/treatments-agent/3803519f-d505-4aef-82c3-5cfd2178c30b/", "uuid": "3803519f-d505-4aef-82c3-5cfd2178c30b", "status": "released", "treatment_type": "Transient Transfection", "description": "Electroporation of preassembled Cas9-gRNA RNP using a light deactivatable photocleavable AluGG-pcRNA", "constructs": [{"uuid": "55af3fe7-9c8b-412a-80c1-ccf79dbbda74", "name": "AluGG-pcRNA", "display_title": "AluGG-pcRNA", "@type": ["Construct", "Item"], "@id": "/constructs/55af3fe7-9c8b-412a-80c1-ccf79dbbda74/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "Light (1.0h)", "duration": 1.0, "@type": ["TreatmentAgent", "Treatment", "Item"], "@id": "/treatments-agent/33573727-88d8-40ad-a4c6-b2e27b111771/", "duration_units": "hour", "uuid": "33573727-88d8-40ad-a4c6-b2e27b111771", "status": "released", "treatment_type": "Light", "description": "1 hour light exposure", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "cell_culture_details": [{"uuid": "7ebd6388-d48f-489a-b826-e0e8be0518eb", "status": "released", "@id": "/biosample-cell-cultures/7ebd6388-d48f-489a-b826-e0e8be0518eb/", "in_vitro_differentiated": "No", "display_title": "BiosampleCellCulture from 2022-02-14", "@type": ["BiosampleCellCulture", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "badges": [{"messages": ["Biosample missing morphology_image"], "badge": {"badge_icon": "/static/img/badges/biosample-icon.svg", "title": "Biosample Metadata Incomplete", "display_title": "Biosample Metadata Incomplete", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "@type": ["Badge", "Item"], "warning": "Biosample Metadata Incomplete", "badge_classification": "Warning", "status": "released", "@id": "/badges/biosample-metadata-incomplete/", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_type": {"uuid": "5b35245d-5777-4983-b7e8-8dffd9ab83ab", "status": "released", "assay_subclass_short": "Open Chromatin", "assay_subclassification": "Open Chromatin", "title": "ATAC-seq", "@type": ["ExperimentType", "Item"], "experiment_category": "Sequencing", "display_title": "ATAC-seq", "assay_classification": "Linear DNA Enrichment", "@id": "/experiment-types/atac-seq/", "other_tags": ["1D"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "experiment_categorizer": {"field": "Default"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2022-03-14T16:16:48.186576+00:00"}}], "experimentset_type": "replicate", "completed_processes": ["ENCODE_ATAC_Pipeline_1.1.1"], "@id": "/experiment-set-replicates/4DNESRIVHLUJ/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "b90db6a2-2270-4680-bd52-f14b9e2c0c4b", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNESRIVHLUJ", "external_references": [], "produced_in_pub": {"@id": "/publications/d25a0018-2b8a-4f15-9e5f-ffa2f77420ab/", "short_attribution": "Zou RS et al. (2022)", "journal": "Nature cell biology", "uuid": "d25a0018-2b8a-4f15-9e5f-ffa2f77420ab", "display_title": "Zou RS et al. (2022) PMID:36064968", "ID": "PMID:36064968", "abstract": "Here we present an approach that combines a clustered regularly interspaced short palindromic repeats (CRISPR) system that simultaneously targets hundreds of epigenetically diverse endogenous genomic sites with high-throughput sequencing to measure Cas9 dynamics and cellular responses at scale. This massive multiplexing of CRISPR is enabled by means of multi-target guide RNAs (mgRNAs), degenerate guide RNAs that direct Cas9 to a pre-determined number of well-mapped  sites. mgRNAs uncovered generalizable insights into Cas9 binding and cleavage, revealing rapid post-cleavage Cas9 departure and repair factor loading at protospacer adjacent motif-proximal genomic DNA. Moreover, by bypassing confounding effects from guide RNA sequence, mgRNAs unveiled that Cas9 binding is enhanced at chromatin-accessible regions, and cleavage by bound Cas9 is more efficient near transcribed regions. Combined with light-mediated activation and deactivation of Cas9 activity, mgRNAs further enabled high-throughput study of the cellular response to double-strand breaks with high temporal resolution, revealing the presence, extent (under 2 kb) and kinetics (~1 h) of reversible DNA damage-induced chromatin decompaction. Altogether, this work establishes mgRNAs as a generalizable platform for multiplexing CRISPR and advances our understanding of intracellular Cas9 activity and the DNA damage response at endogenous loci.", "@type": ["Publication", "Item"], "title": "Massively parallel genomic perturbations with multi-target CRISPR interrogates Cas9 activity and DNA repair at endogenous sites.", "url": "https://www.ncbi.nlm.nih.gov/pubmed/36064968", "status": "current", "authors": ["Zou RS", "Marin-Gonzalez A", "Liu Y", "Liu HB", "Shen L", "Dveirin RK", "Luo JXJ", "Kalhor R", "Ha T"], "date_published": "2022-09-05", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "pubs_using": [], "publications_of_set": [{"abstract": "Here we present an approach that combines a clustered regularly interspaced short palindromic repeats (CRISPR) system that simultaneously targets hundreds of epigenetically diverse endogenous genomic sites with high-throughput sequencing to measure Cas9 dynamics and cellular responses at scale. This massive multiplexing of CRISPR is enabled by means of multi-target guide RNAs (mgRNAs), degenerate guide RNAs that direct Cas9 to a pre-determined number of well-mapped  sites. mgRNAs uncovered generalizable insights into Cas9 binding and cleavage, revealing rapid post-cleavage Cas9 departure and repair factor loading at protospacer adjacent motif-proximal genomic DNA. Moreover, by bypassing confounding effects from guide RNA sequence, mgRNAs unveiled that Cas9 binding is enhanced at chromatin-accessible regions, and cleavage by bound Cas9 is more efficient near transcribed regions. Combined with light-mediated activation and deactivation of Cas9 activity, mgRNAs further enabled high-throughput study of the cellular response to double-strand breaks with high temporal resolution, revealing the presence, extent (under 2 kb) and kinetics (~1 h) of reversible DNA damage-induced chromatin decompaction. Altogether, this work establishes mgRNAs as a generalizable platform for multiplexing CRISPR and advances our understanding of intracellular Cas9 activity and the DNA damage response at endogenous loci.", "ID": "PMID:36064968", "title": "Massively parallel genomic perturbations with multi-target CRISPR interrogates Cas9 activity and DNA repair at endogenous sites.", "@type": ["Publication", "Item"], "date_published": "2022-09-05", "@id": "/publications/d25a0018-2b8a-4f15-9e5f-ffa2f77420ab/", "uuid": "d25a0018-2b8a-4f15-9e5f-ffa2f77420ab", "journal": "Nature cell biology", "authors": ["Zou RS", "Marin-Gonzalez A", "Liu Y", "Liu HB", "Shen L", "Dveirin RK", "Luo JXJ", "Kalhor R", "Ha T"], "status": "current", "display_title": "Zou RS et al. (2022) PMID:36064968", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "number_of_experiments": 2, "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBS86B5OZD/", "embedded_path": "experiments_in_set.biosample.badges", "item": {"messages": ["Biosample missing morphology_image"], "badge": {"commendation": null, "warning": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@id": "/badges/biosample-metadata-incomplete/", "badge_icon": "/static/img/badges/biosample-icon.svg", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group."}}}, {"parent": "/biosamples/4DNBSEPLZJ1Y/", "embedded_path": "experiments_in_set.biosample.badges", "item": {"messages": ["Biosample missing morphology_image"], "badge": {"commendation": null, "warning": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@id": "/badges/biosample-metadata-incomplete/", "badge_icon": "/static/img/badges/biosample-icon.svg", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group."}}}]}, "validation-errors": []}