{"lab": {"@type": ["Lab", "Item"], "status": "current", "display_title": "Bing Ren, UCSD", "correspondence": [{"contact_email": "YmlyZW5AdWNzZC5lZHU=", "@id": "/users/e3159ffc-a5a9-43a1-8cfa-90b776c39788/", "display_title": "Bing Ren"}], "title": "Bing Ren, UCSD", "@id": "/labs/bing-ren-lab/", "uuid": "795847de-20b6-4f8c-ba8d-185215469cbf", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.795847de-20b6-4f8c-ba8d-185215469cbf"]}}, "award": {"display_title": "SAN DIEGO CENTER FOR 4D NUCLEOME RESEARCH", "uuid": "4871e338-b07d-4665-a00a-357648e5bad6", "@id": "/awards/1U54DK107977-01/", "project": "4DN", "@type": ["Award", "Item"], "description": "NOFIC: The complete sequencing of the human genome has provided an unprecedented opportunity for the study of the structure and function of the human genome. While our genome has historically been viewed as a linear sequence of bases, it has progressively become clear that this is an inadequate way to represent our genetic information. Notably, research over the last 30 years has begun to shed light on the fact that the higher-order, 3-dimensional organization of our genome plays a critical role in the interpretation of the genetic information encoded in our genome. The structure of our genome in the nucleus has been clearly demonstrated to play influential roles in diverse nuclear processes including DNA replication and gene expression. Despite this, our understanding of the structure of our genome within the nucleus remains incomplete. The reasons for this include limitations in the resolution and throughput of existing tools in chromatin topology mapping, a scarcity of the analytical tools for studying genome structure datasets, and the difficulty to relate the nuclear structure to function. Due to recent advancements in molecular methods based on high-throughput DNA sequencing, single cell analytical approaches, and high-resolution microscopy, the time for breaking through these previous limitations has come. We will establish a highly collaborative, innovative team in order to develop the tools necessary to transform our understanding of chromatin architecture and function in mammalian cells. We will begin by developing datasets that establish gold standards for the study of nuclear structure and function using genetic, biochemical and imaging approaches. We will optimize current existing technologies for mapping genome wide chromatin interactions, while also developing novel, complementary approaches for studying chromatin structure. We will also develop innovative analytical methods to interpret the chromatin structural data, unraveling principles of structural- and temporal- chromatin organization. Our highly collaborative team will draw on the diverse experiences of its members to provide a synergistic environment to push the limits of our understanding of nuclear structure. We expect that the tools and datasets generated through the proposed research will dramatically advance our understanding of the chromatin structure and function in human cells.", "name": "1U54DK107977-01", "status": "current", "center_title": "NOFIC - Ren", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "files": [{"file_classification": "raw file", "dbxrefs": ["SRA:SRR7807464"], "status": "released", "@id": "/files-fastq/4DNFI8YG3FVD/", "file_type": "reads", "accession": "4DNFI8YG3FVD", "href": "/files-fastq/4DNFI8YG3FVD/@@download/4DNFI8YG3FVD.fastq.gz", "file_size": 29670518698, "upload_key": "5c981a66-6730-48e9-aa5c-7bf831704f49/4DNFI8YG3FVD.fastq.gz", "paired_end": "1", "uuid": "5c981a66-6730-48e9-aa5c-7bf831704f49", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFI8YG3FVD.fastq.gz", "file_type_detailed": "reads (fastq)", "related_files": [{"relationship_type": "paired with", "file": {"uuid": "541b4530-cf3b-4260-81ac-e5c309d0a8f7", "display_title": "4DNFI95L3LI8.fastq.gz", "file_type_detailed": "reads (fastq)", "accession": "4DNFI95L3LI8", "status": "released", "file_type": "reads", "@id": "/files-fastq/4DNFI95L3LI8/", "@type": ["FileFastq", "File", "Item"], "paired_end": "2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric": {"@id": "/quality-metrics-fastqc/bb20379b-a645-4949-b7b2-82a0e22174a6/", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI8YG3FVD/fastqc_report.html", "status": "released", "overall_quality_status": "PASS", "Total Sequences": 588712384, "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "display_title": "QualityMetricFastqc from 2018-10-03", "Sequence length": "35-101", "uuid": "bb20379b-a645-4949-b7b2-82a0e22174a6", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"status": "released", "file_format": "fastq", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [{"ref": "SRA:SRR7807464", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR7807464"}]}, {"file_classification": "raw file", "dbxrefs": ["SRA:SRR7807464"], "status": "released", "@id": "/files-fastq/4DNFI95L3LI8/", "file_type": "reads", "accession": "4DNFI95L3LI8", "href": "/files-fastq/4DNFI95L3LI8/@@download/4DNFI95L3LI8.fastq.gz", "file_size": 31803419431, "upload_key": "541b4530-cf3b-4260-81ac-e5c309d0a8f7/4DNFI95L3LI8.fastq.gz", "paired_end": "2", "uuid": "541b4530-cf3b-4260-81ac-e5c309d0a8f7", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFI95L3LI8.fastq.gz", "file_type_detailed": "reads (fastq)", "related_files": [{"relationship_type": "paired with", "file": {"uuid": "5c981a66-6730-48e9-aa5c-7bf831704f49", "display_title": "4DNFI8YG3FVD.fastq.gz", "file_type_detailed": "reads (fastq)", "accession": "4DNFI8YG3FVD", "status": "released", "file_type": "reads", "@id": "/files-fastq/4DNFI8YG3FVD/", "@type": ["FileFastq", "File", "Item"], "paired_end": "1", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric": {"@id": "/quality-metrics-fastqc/08d29325-afc4-4114-8a21-f45984599321/", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI95L3LI8/fastqc_report.html", "status": "released", "overall_quality_status": "PASS", "Total Sequences": 588712384, "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "display_title": "QualityMetricFastqc from 2018-10-03", "Sequence length": "35-101", "uuid": "08d29325-afc4-4114-8a21-f45984599321", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"status": "released", "file_format": "fastq", "display_title": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [{"ref": "SRA:SRR7807464", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR7807464"}]}], "notes": "Old Target: 3e29da86-f46f-4f13-a709-0e6affa64ed6", "status": "released", "aliases": ["ren:F123_B1_H3K4me3_PLACseq"], "dbxrefs": ["GEO:GSM3380554", "SRA:SRX4659159"], "antibody": {"antibody_name": "anti-H3K4me3", "display_title": "anti-H3K4me3 (Millipore Sigma, 04-745)", "status": "released", "antibody_product_no": "04-745", "@type": ["Antibody", "Item"], "uuid": "18be09e1-629f-4f6e-9097-84bd6860048f", "@id": "/antibodys/anti-H3K4me3-04-745/", "antibody_vendor": {"status": "released", "display_title": "Millipore Sigma", "@id": "/vendors/millipore-sigma/", "title": "Millipore Sigma", "uuid": "255e81a2-6654-4d8b-8359-59f87c071d65", "@type": ["Vendor", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "protocol": {"@id": "/protocols/43dcd86e-117c-4c7a-8d6f-cb8e30395151/", "display_title": "PLAC-seq%20protocol_10162017_Ren%20lab.pdf", "status": "released", "@type": ["Protocol", "Item"], "uuid": "43dcd86e-117c-4c7a-8d6f-cb8e30395151", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNEXZSEZ9GH", "biosample": {"uuid": "a4dec072-6cd4-4fb6-9bb7-f0083db1ec30", "display_title": "4DNBSUWJ2K85", "status": "released", "modifications_summary": "None", "accession": "4DNBSUWJ2K85", "biosample_type": "stem cells", "@id": "/biosamples/4DNBSUWJ2K85/", "biosource_summary": "F123-CASTx129 (Tier 2)", "treatments_summary": "None", "@type": ["Biosample", "Item"], "biosource": [{"lab": {"@type": ["Lab", "Item"], "status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "@id": "/labs/4dn-dcic-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "award": {"@id": "/awards/1U01CA200059-01/", "@type": ["Award", "Item"], "status": "current", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "tissue": {"status": "released", "synonyms": ["animal stem cell"], "@id": "/ontology-terms/CL:0000034/", "slim_terms": [{"@id": "/ontology-terms/GO:0005623/", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/CL:0000000/", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "term_name": "stem cell", "preferred_name": "stem cell", "@type": ["OntologyTerm", "Item"], "term_id": "CL:0000034", "display_title": "stem cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "aliases": ["dcic:f123castx129T2", "4dn-dcic-lab:f123castx129T2"], "accession": "4DNSRTNKUDSA", "cell_line": {"@id": "/ontology-terms/EFO:0009319/", "uuid": "b75930ee-182a-4f7a-8360-ecd6b7ac532f", "synonyms": ["F123"], "preferred_name": "F123-CASTx129", "display_title": "F123-CASTx129", "slim_terms": [{"display_title": "cell", "@id": "/ontology-terms/GO:0005623/", "status": "current", "@type": ["OntologyTerm", "Item"], "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "@id": "/ontology-terms/CL:0000000/", "status": "released", "@type": ["OntologyTerm", "Item"], "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "term_name": "F123-CASTx129", "@type": ["OntologyTerm", "Item"], "term_id": "EFO:0009319", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"display_title": "4DNINWEP34C1", "uuid": "9eb64afa-705f-4710-a298-32ad67764d14", "@id": "/individuals-mouse/4DNINWEP34C1/", "status": "released", "@type": ["IndividualMouse", "Individual", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "references": [], "description": "Castx129 male mouse hybrid ES cells - clone F123.  Maternal 129/Sv, Paternal CAST", "date_created": "2017-04-10T01:14:07.548943+00:00", "submitted_by": {"error": "no view permissions"}, "SOP_cell_line": {"uuid": "1d39b581-9200-4494-8b24-3dc77d595bbb", "status": "released", "@id": "/protocols/1d39b581-9200-4494-8b24-3dc77d595bbb/", "@type": ["Protocol", "Item"], "display_title": "4DN_F123_SOP_170425.pdf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2023-07-11T18:22:47.952481+00:00"}, "modifications": [], "biosource_type": "stem cell derived cell line", "cell_line_tier": "Tier 2", "public_release": "2017-04-10T01:14:07.548943+00:00", "schema_version": "2", "project_release": "2017-04-10T01:14:07.548943+00:00", "biosource_vendor": {"uuid": "e909af70-74cb-426a-8ecf-1c9100c1ea44", "@type": ["Vendor", "Item"], "status": "released", "display_title": "Bing Ren Lab", "@id": "/vendors/bing-ren-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "alternate_accessions": [], "@id": "/biosources/4DNSRTNKUDSA/", "@type": ["Biosource", "Item"], "uuid": "f8ddbc70-a311-490b-b0ef-7549868a059c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "F123-CASTx129 (Tier 2) - 4DNSRTNKUDSA", "external_references": [], "biosource_name": "F123-CASTx129 (Tier 2)", "biosource_category": ["Tier 2", "Mouse stem cell"], "organism": {"@type": ["Organism", "Item"], "display_title": "M. musculus", "@id": "/organisms/10090/", "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "status": "released", "name": "mouse", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "badges": [{"messages": ["Biosample missing morphology_image", "Biosample is a stem cell line over 10 passages but missing karyotype"], "badge": {"status": "released", "badge_classification": "Warning", "display_title": "Biosample Metadata Incomplete", "@id": "/badges/biosample-metadata-incomplete/", "warning": "Biosample Metadata Incomplete", "badge_icon": "/static/img/badges/biosample-icon.svg", "title": "Biosample Metadata Incomplete", "@type": ["Badge", "Item"], "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "pcr_cycles": 12, "description": "H3K4me3 PLAC-seq on F123 cells, biological replicate 1", "follows_sop": "No", "sop_mapping": {"has_sop": "No"}, "date_created": "2018-09-21T18:05:25.860445+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2021-01-26T19:47:50.802086+00:00"}, "ligation_time": 120, "biotin_removed": "No", "digestion_time": 120, "public_release": "2018-10-02", "schema_version": "5", "experiment_type": {"status": "released", "title": "PLAC-seq", "display_title": "PLAC-seq", "@id": "/experiment-types/plac-seq/", "experiment_category": "Sequencing", "assay_subclass_short": "IP-based 3C", "uuid": "f2b74c1b-37b5-43b0-acf0-c2e2bba961d7", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "ligation_volume": 1.2, "processed_files": [{"@type": ["FileProcessed", "File", "Item"], "uuid": "6282f0c7-3d24-4325-bb73-1f5b7e134948", "file_format": {"@type": ["FileFormat", "Item"], "file_format": "bam", "@id": "/file-formats/bam/", "display_title": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "display_title": "4DNFIR2SSMW1.bam", "file_type_detailed": "alignments (bam)", "file_size": 89339960333, "file_classification": "processed file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/6282f0c7-3d24-4325-bb73-1f5b7e134948/4DNFIR2SSMW1.bam", "status": "released", "href": "/files-processed/4DNFIR2SSMW1/@@download/4DNFIR2SSMW1.bam", "upload_key": "6282f0c7-3d24-4325-bb73-1f5b7e134948/4DNFIR2SSMW1.bam", "@id": "/files-processed/4DNFIR2SSMW1/", "file_type": "alignments", "accession": "4DNFIR2SSMW1", "quality_metric": {"display_title": "QualityMetricBamqc from 2020-01-17", "overall_quality_status": "PASS", "@id": "/quality-metrics-bamqc/12f3e8e3-dfa6-4c10-87d6-460233c6c23b/", "status": "released", "uuid": "12f3e8e3-dfa6-4c10-87d6-460233c6c23b", "@type": ["QualityMetricBamqc", "QualityMetric", "Item"], "quality_metric_summary": [{"title": "Total Reads", "value": "588712384", "numberType": "integer"}, {"title": "Unmapped Reads", "value": "12.819", "tooltip": "Percent of total reads (=75.47m)", "numberType": "percent"}, {"title": "Multimapped Reads", "value": "17.752", "tooltip": "Percent of total reads (=104.51m)", "numberType": "percent"}, {"title": "Duplicate Reads", "value": "32.731", "tooltip": "Percent of total reads (=192.69m)", "numberType": "percent"}, {"title": "Walks", "value": "5.832", "tooltip": "Percent of total reads (=34.34m)", "numberType": "percent"}, {"title": "Minor Contigs", "value": "0.063", "tooltip": "Percent of total reads (=0.37m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Bing Ren, UCSD", "experiment_type": "PLAC-seq", "experiment_bucket": "processed file", "assay_info": "H3K4me3", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F123-CASTx129 (Tier 2)", "lab_name": "4DN DCIC, HMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}, {"@type": ["FileProcessed", "File", "Item"], "uuid": "8458e646-e0d4-4c42-912d-f46f331d934f", "file_format": {"@type": ["FileFormat", "Item"], "file_format": "pairs", "@id": "/file-formats/pairs/", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "display_title": "4DNFIIHRFVI3.pairs.gz", "file_type_detailed": "contact list-replicate (pairs)", "file_size": 3678423390, "file_classification": "processed file", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/8458e646-e0d4-4c42-912d-f46f331d934f/4DNFIIHRFVI3.pairs.gz", "status": "released", "href": "/files-processed/4DNFIIHRFVI3/@@download/4DNFIIHRFVI3.pairs.gz", "upload_key": "8458e646-e0d4-4c42-912d-f46f331d934f/4DNFIIHRFVI3.pairs.gz", "@id": "/files-processed/4DNFIIHRFVI3/", "file_type": "contact list-replicate", "accession": "4DNFIIHRFVI3", "quality_metric": {"display_title": "QualityMetricPairsqc from 2018-12-06", "Total reads": 181708490, "overall_quality_status": "PASS", "@id": "/quality-metrics-pairsqc/e26427f3-f59b-4cc0-8e76-8ca0bf7c97e1/", "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIIHRFVI3/pairsqc_report.html", "uuid": "e26427f3-f59b-4cc0-8e76-8ca0bf7c97e1", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "quality_metric_summary": [{"title": "Filtered Reads", "value": "181708490", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "51.724", "tooltip": "Percent of filtered reads (=93.99m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "37.665", "tooltip": "Percent of filtered reads (=68.44m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "10.61", "tooltip": "Percent of filtered reads (=19.28m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Bing Ren, UCSD", "experiment_type": "PLAC-seq", "experiment_bucket": "processed file", "assay_info": "H3K4me3", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F123-CASTx129 (Tier 2)", "lab_name": "4DN DCIC, HMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}], "project_release": "2018-10-02", "targeted_factor": [{"@type": ["BioFeature", "Item"], "uuid": "3a28616d-d4aa-49de-b42c-56e465ee9d63", "@id": "/bio-features/3a28616d-d4aa-49de-b42c-56e465ee9d63/", "status": "released", "display_title": "H3K4me3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "digestion_enzyme": {"uuid": "d8da42d0-bc20-40e5-bacf-c263b8603e03", "@type": ["Enzyme", "Item"], "display_title": "MboI", "@id": "/enzymes/MboI/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "crosslinking_time": 15, "enzyme_lot_number": "NA", "biosample_quantity": 1300000, "crosslinking_method": "1% Formaldehyde", "fragment_size_range": "300-800", "fragmentation_method": "shearing", "ligation_temperature": 23, "average_fragment_size": 400, "digestion_temperature": 37, "biosample_quantity_units": "cells", "crosslinking_temperature": 23, "library_preparation_date": "2016-07-13", "fragment_size_selection_method": "SPRI beads", "@id": "/experiments-chiapet/4DNEXZSEZ9GH/", "@type": ["ExperimentChiapet", "Experiment", "Item"], "uuid": "c4662c7d-bd8a-4144-a852-ac4cfd91c084", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "PLAC-seq against H3K4me3 on F123-CASTx129 (Tier 2) - 4DNEXZSEZ9GH", "external_references": [{"ref": "GEO:GSM3380554", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3380554"}, {"ref": "SRA:SRX4659159", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRX4659159"}], "experiment_sets": [{"experimentset_type": "replicate", "@id": "/experiment-set-replicates/4DNESVMWQH93/", "status": "released", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "e5268f07-1bc4-4574-bd31-81f87ba3dea5", "accession": "4DNESVMWQH93", "display_title": "4DNESVMWQH93", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "produced_in_pub": {"@type": ["Publication", "Item"], "date_published": "2019-04", "ID": "PMID:30986246", "authors": ["Juric I", "Yu M", "Abnousi A", "Raviram R", "Fang R", "Zhao Y", "Zhang Y", "Qiu Y", "Yang Y", "Li Y", "Ren B", "Hu M"], "title": "MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments.", "journal": "PLoS computational biology", "status": "current", "short_attribution": "Juric I et al. (2019)", "@id": "/publications/d7d5ebaf-64d0-4556-b56a-a49af7577e31/", "abstract": "Hi-C and chromatin immunoprecipitation (ChIP) have been combined to identify long-range chromatin interactions genome-wide at reduced cost and enhanced resolution, but extracting information from the resulting datasets has been challenging. Here we describe a computational method, MAPS, Model-based Analysis  of PLAC-seq and HiChIP, to process the data from such experiments and identify long-range chromatin interactions. MAPS adopts a zero-truncated Poisson regression framework to explicitly remove systematic biases in the PLAC-seq and HiChIP datasets, and then uses the normalized chromatin contact frequencies to identify significant chromatin interactions anchored at genomic regions bound by  the protein of interest. MAPS shows superior performance over existing software tools in the analysis of chromatin interactions from multiple PLAC-seq and HiChIP datasets centered on different transcriptional factors and histone marks. MAPS is freely available at https://github.com/ijuric/MAPS.", "uuid": "d7d5ebaf-64d0-4556-b56a-a49af7577e31", "display_title": "Juric I et al. (2019) PMID:30986246", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "publications_of_exp": [{"uuid": "d7d5ebaf-64d0-4556-b56a-a49af7577e31", "authors": ["Juric I", "Yu M", "Abnousi A", "Raviram R", "Fang R", "Zhao Y", "Zhang Y", "Qiu Y", "Yang Y", "Li Y", "Ren B", "Hu M"], "journal": "PLoS computational biology", "@type": ["Publication", "Item"], "status": "current", "display_title": "Juric I et al. (2019) PMID:30986246", "date_published": "2019-04", "title": "MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments.", "abstract": "Hi-C and chromatin immunoprecipitation (ChIP) have been combined to identify long-range chromatin interactions genome-wide at reduced cost and enhanced resolution, but extracting information from the resulting datasets has been challenging. Here we describe a computational method, MAPS, Model-based Analysis  of PLAC-seq and HiChIP, to process the data from such experiments and identify long-range chromatin interactions. MAPS adopts a zero-truncated Poisson regression framework to explicitly remove systematic biases in the PLAC-seq and HiChIP datasets, and then uses the normalized chromatin contact frequencies to identify significant chromatin interactions anchored at genomic regions bound by  the protein of interest. MAPS shows superior performance over existing software tools in the analysis of chromatin interactions from multiple PLAC-seq and HiChIP datasets centered on different transcriptional factors and histone marks. MAPS is freely available at https://github.com/ijuric/MAPS.", "short_attribution": "Juric I et al. (2019)", "ID": "PMID:30986246", "@id": "/publications/d7d5ebaf-64d0-4556-b56a-a49af7577e31/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_categorizer": {"field": "Target", "value": "H3K4me3", "combined": "Target: H3K4me3"}, "experiment_summary": "PLAC-seq against H3K4me3 on F123-CASTx129 (Tier 2)", "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSUWJ2K85/", "embedded_path": "biosample.badges", "item": {"messages": ["Biosample missing morphology_image", "Biosample is a stem cell line over 10 passages but missing karyotype"], "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": []}