{"lab": {"title": "Sheng Zhong, UCSD", "display_title": "Sheng Zhong, UCSD", "@id": "/labs/sheng-zhong-lab/", "correspondence": [{"contact_email": "c3pob25nQHVjc2QuZWR1", "@id": "/users/5549e16d-fa63-477c-a1ed-6189cecc1304/", "display_title": "Sheng Zhong"}], "status": "current", "uuid": "3452dfa5-ee8b-4dbc-8068-00cadde268b9", "@type": ["Lab", "Item"], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3452dfa5-ee8b-4dbc-8068-00cadde268b9"]}}, "tags": ["4DN Joint Analysis 2018"], "award": {"@type": ["Award", "Item"], "status": "current", "@id": "/awards/1U01CA200147-01/", "uuid": "c55dd1f0-433b-4714-bfce-8b3ae09f071c", "display_title": "THE ORGANIZATIONAL HUB AND WEB PORTAL FOR THE 4D NUCLEOME NETWORK", "center_title": "OH - Zhong", "description": "OH: Recent technological developments have significantly advanced our understanding of the three-dimensional organization of the nucleus. It has also become increasingly clear that the 3D nucleome plays an important role in regulating gene expression. Large cohorts of data are being generated to investigate the impact of the temporal changes of nuclear organization (the 4D nucleome) to normal development and disease processes. The primary goal of this proposal is the creation of an effective organizational hub and web portal for the 4D nucleome. We also propose to develop an effective coordination structure for the 4D nucleome activities. First, we will develop and organize effective networking methods and consortium meetings for establishing protocols and standards. We will develop a framework for coordination of the funded 4D nucleome projects. We will organize annual consortium-wide grantees meeting. We will utilize the professional organizers who have previously worked with the PIs and the premium conference venues at Atkinson Hall in UCSD (http://www.calit2.net). Two major activities will be organized during the annual meeting. Second, we will develop an adaptable, scalable, and user-friendly 4DN web portal. We will build the 4DN Network community web portal and a Virtual Resource Repository. This portal will be an integrated, versatile, and inter-operable data management, retrieval, analysis, and visualization system. We will leverage the ENCODE Comparative Browser (http://encode.cepbrowser.org) for developing the 4D network portal. In addition, the portal will incorporate data generated from outside the consortium, publish E-manuals for the consortium-agreed protocols, and provide the most up-to-date information on the data clearance. Third, we will coordinate and manage the 4DN Network Opportunity Pool. The opportunity pool of funds will be distributed and managed with 100% transparency. Competitive distribution with the funds will be coordinated by a professional manager with extensive experience in managing Center and Training Grants. Fourth, we will develop a comprehensive strategy for training and outreach. The proposed unit will aim to regularly train and update 4DN research network members and collaborators in several key areas including: 1) new technologies; 2) data/sample collection protocols; 3) data analysis methods; 4) data submission protocols; 5) data retrieval methods; 6) data QA/QC; 7) data exchange standards and data ontologies; 8) the contents of different 4DN and public databases; 9) data privacy and 10) data dissemination.", "name": "1U01CA200147-01", "project": "4DN", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "replaced", "aliases": ["zhong-lab:ExperimentSet_HFFc6_MARGI"], "accession": "4DNESJC437VS", "description": "Mapping RNA-genome interactions in HFFc6 cell line using MARGI technology", "date_created": "2018-04-19T18:54:49.206863+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-01-28T17:09:38.732940+00:00"}, "public_release": "2018-08-24", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"@type": ["ExperimentSeq", "Experiment", "Item"], "status": "archived", "accession": "4DNEXWXUC1X2", "@id": "/experiments-seq/4DNEXWXUC1X2/", "display_title": "MARGI on HFFc6 (Tier 1) - 4DNEXWXUC1X2", "uuid": "0ba3f165-7f78-4d57-a6bd-e7403bfd8631", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 1, "tec_rep_no": 2, "replicate_exp": {"@type": ["ExperimentSeq", "Experiment", "Item"], "status": "archived", "accession": "4DNEX21WVKWL", "@id": "/experiments-seq/4DNEX21WVKWL/", "display_title": "MARGI on HFFc6 (Tier 1) - 4DNEX21WVKWL", "uuid": "9bba36e4-069b-4cc2-b8e7-b121508803c1", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "static_headers": [{"lab": {"status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "@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"]}}, "body": "\n**Data Use Guidelines:** This is a data set generated by the \n4DN Network and made freely available to the scientific \ncommunity. If you are intending to use these data for a \npublication, we ask that you please contact the data \ngenerating lab to discuss possible coordinated publication. \nIn your manuscript, please cite the 4DN White Paper \n([doi:10.1038/nature23884](https://doi.org/10.1038/nature23884)) \nand the 4DN Data Portal paper \n([doi:10.1038/s41467-022-29697-4](https://doi.org/10.1038/s41467-022-29697-4)), \nand please acknowledge the 4DN lab which generated the data. Please direct any questions to the [Data Coordination and Integration Center](mailto:support@4dnucleome.org).", "name": "item-page-headers.ExperimentSet.data-usage-guidelines", "award": {"@type": ["Award", "Item"], "@id": "/awards/1U01CA200059-01/", "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"]}}, "title": "Data Usage Guidelines", "status": "released", "aliases": [], "options": {"filetype": "md", "title_icon": "exclamation-circle", "collapsible": false, "default_open": true}, "date_created": "2018-08-06T03:09:55.543206+00:00", "section_type": "Item Page Header", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2022-05-09T09:31:34.537494+00:00"}, "schema_version": "2", "@id": "/static-sections/621e8359-3885-40ce-965d-91894aa7b758/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "621e8359-3885-40ce-965d-91894aa7b758", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267228139"]}, "display_title": "Data Usage Guidelines", "external_references": [], "content": "\n**Data Use Guidelines:** This is a data set generated by the \n4DN Network and made freely available to the scientific \ncommunity. If you are intending to use these data for a \npublication, we ask that you please contact the data \ngenerating lab to discuss possible coordinated publication. \nIn your manuscript, please cite the 4DN White Paper \n([doi:10.1038/nature23884](https://doi.org/10.1038/nature23884)) \nand the 4DN Data Portal paper \n([doi:10.1038/s41467-022-29697-4](https://doi.org/10.1038/s41467-022-29697-4)), \nand please acknowledge the 4DN lab which generated the data. Please direct any questions to the [Data Coordination and Integration Center](mailto:support@4dnucleome.org).", "filetype": "md", "content_as_html": "<div class=\"markdown-container\"><p><strong>Data Use Guidelines:</strong> This is a data set generated by the \n4DN Network and made freely available to the scientific \ncommunity. If you are intending to use these data for a \npublication, we ask that you please contact the data \ngenerating lab to discuss possible coordinated publication. \nIn your manuscript, please cite the 4DN White Paper \n(<a href=\"https://doi.org/10.1038/nature23884\" rel=\"noopener noreferrer\" target=\"_blank\">doi:10.1038/nature23884</a>) \nand the 4DN Data Portal paper \n(<a href=\"https://doi.org/10.1038/s41467-022-29697-4\" rel=\"noopener noreferrer\" target=\"_blank\">doi:10.1038/s41467-022-29697-4</a>), \nand please acknowledge the 4DN lab which generated the data. Please direct any questions to the <a href=\"mailto:support@4dnucleome.org\">Data Coordination and Integration Center</a>.</p></div>"}, {"lab": {"status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "@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"]}}, "body": "**MARGI**\n\nMARGI is a method to map native RNA-DNA interactions from unperturbed cells at a global scale. It is a method analogous to the measurement of DNA-DNA interactions  by Hi-C experiments. MARGI was first published in 2017, and since then, the protocol has been rapidly improved. MARGI 2.0 is the latest version that introduced RNA-DNA proximity ligation *in situ* inside intact nuclei instead of in solution in order to reduce the rate of random ligation. In addition, this version also reduces the necessary amount of cell input 100-fold and shortens experimental processing time.\n\nThe protocol involves crosslinking the cells with formaldehyde to form links between physically adjacent RNA-DNA molecules. The intact nuclei are collected from fixed cells and permeabilized with SDS. A restriction enzyme (AluI) is used to digest chromatin into DNA fragments and RNase I is used to fragment RNA. A specially designed biotinylated linker is introduced to ligate to 3\u00b4-end of RNA first and then this RNA-ligated linker is ligated to DNA. These ligation steps are controlled by the configuration of the linker and by sequential applications of different end modifications and ligation enzymes. Nuclei are lysed, and successfully ligated products, in the form of RNA-linker-DNA, are selected with streptavidin beads, followed by converting the RNA part of the chimera into cDNA on beads. cDNA-linker-DNA is circularized and then cut in the middle, producing DNAs with the configuration left.half.Linker-RNA-DNA-right.half.Linker, which are subjected to library amplification and paired-end sequencing.\n\n<div> \n<img style=\"width:400px;\" src=\"https://s3.amazonaws.com/4dn-dcic-public/static-pages/InfoBoxes/MARGI2.png\" />\n    <br/><br/>\n    <em> Image Source: Weixin Wu, Xingzhao Wen, Sheng Zhong, private communication </em>\n</div>                                                                                                              \n", "name": "item-page-headers.ExperimentType.margi", "award": {"@type": ["Award", "Item"], "@id": "/awards/1U01CA200059-01/", "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"]}}, "title": "Assay Description", "status": "released", "aliases": ["4dn-dcic-lab:4dn-dcic-lab:4dn-dcic-lab:experiment_infobox_margi"], "options": {"filetype": "md", "collapsible": false, "default_open": false}, "date_created": "2018-09-20T19:17:26.139621+00:00", "section_type": "Item Page Header", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-05-15T16:58:04.692266+00:00"}, "schema_version": "2", "@id": "/static-sections/0c2ba23e-b256-47ce-a37c-0f1282471789/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "0c2ba23e-b256-47ce-a37c-0f1282471789", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.56c9c683-bb11-471b-b590-c656f7dc03c1"]}, "display_title": "Assay Description", "external_references": [], "content": "**MARGI**\n\nMARGI is a method to map native RNA-DNA interactions from unperturbed cells at a global scale. It is a method analogous to the measurement of DNA-DNA interactions  by Hi-C experiments. MARGI was first published in 2017, and since then, the protocol has been rapidly improved. MARGI 2.0 is the latest version that introduced RNA-DNA proximity ligation *in situ* inside intact nuclei instead of in solution in order to reduce the rate of random ligation. In addition, this version also reduces the necessary amount of cell input 100-fold and shortens experimental processing time.\n\nThe protocol involves crosslinking the cells with formaldehyde to form links between physically adjacent RNA-DNA molecules. The intact nuclei are collected from fixed cells and permeabilized with SDS. A restriction enzyme (AluI) is used to digest chromatin into DNA fragments and RNase I is used to fragment RNA. A specially designed biotinylated linker is introduced to ligate to 3\u00b4-end of RNA first and then this RNA-ligated linker is ligated to DNA. These ligation steps are controlled by the configuration of the linker and by sequential applications of different end modifications and ligation enzymes. Nuclei are lysed, and successfully ligated products, in the form of RNA-linker-DNA, are selected with streptavidin beads, followed by converting the RNA part of the chimera into cDNA on beads. cDNA-linker-DNA is circularized and then cut in the middle, producing DNAs with the configuration left.half.Linker-RNA-DNA-right.half.Linker, which are subjected to library amplification and paired-end sequencing.\n\n<div> \n<img style=\"width:400px;\" src=\"https://s3.amazonaws.com/4dn-dcic-public/static-pages/InfoBoxes/MARGI2.png\" />\n    <br/><br/>\n    <em> Image Source: Weixin Wu, Xingzhao Wen, Sheng Zhong, private communication </em>\n</div>                                                                                                              \n", "filetype": "md", "content_as_html": "<div class=\"markdown-container\"><p><strong>MARGI</strong></p>\n<p>MARGI is a method to map native RNA-DNA interactions from unperturbed cells at a global scale. It is a method analogous to the measurement of DNA-DNA interactions  by Hi-C experiments. MARGI was first published in 2017, and since then, the protocol has been rapidly improved. MARGI 2.0 is the latest version that introduced RNA-DNA proximity ligation <em>in situ</em> inside intact nuclei instead of in solution in order to reduce the rate of random ligation. In addition, this version also reduces the necessary amount of cell input 100-fold and shortens experimental processing time.</p>\n<p>The protocol involves crosslinking the cells with formaldehyde to form links between physically adjacent RNA-DNA molecules. The intact nuclei are collected from fixed cells and permeabilized with SDS. A restriction enzyme (AluI) is used to digest chromatin into DNA fragments and RNase I is used to fragment RNA. A specially designed biotinylated linker is introduced to ligate to 3\u00b4-end of RNA first and then this RNA-ligated linker is ligated to DNA. These ligation steps are controlled by the configuration of the linker and by sequential applications of different end modifications and ligation enzymes. Nuclei are lysed, and successfully ligated products, in the form of RNA-linker-DNA, are selected with streptavidin beads, followed by converting the RNA part of the chimera into cDNA on beads. cDNA-linker-DNA is circularized and then cut in the middle, producing DNAs with the configuration left.half.Linker-RNA-DNA-right.half.Linker, which are subjected to library amplification and paired-end sequencing.</p>\n<div>\n<img src=\"https://s3.amazonaws.com/4dn-dcic-public/static-pages/InfoBoxes/MARGI2.png\" style=\"width:400px;\"/>\n<br/><br/>\n<em> Image Source: Weixin Wu, Xingzhao Wen, Sheng Zhong, private communication </em>\n</div>\n<pre>\n</pre></div>"}, {"lab": {"status": "current", "uuid": "3452dfa5-ee8b-4dbc-8068-00cadde268b9", "@type": ["Lab", "Item"], "@id": "/labs/sheng-zhong-lab/", "display_title": "Sheng Zhong, UCSD", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3452dfa5-ee8b-4dbc-8068-00cadde268b9"]}}, "body": "This experiment set was replaced by [4DNESNGESP28](https://data.4dnucleome.org/experiment-set-replicates/4DNESNGESP28/) because new technical replicates were added.", "name": "static-header.replaced_item_4DNESJC437VS", "award": {"@type": ["Award", "Item"], "@id": "/awards/1U01CA200147-01/", "status": "current", "display_title": "THE ORGANIZATIONAL HUB AND WEB PORTAL FOR THE 4D NUCLEOME NETWORK", "uuid": "c55dd1f0-433b-4714-bfce-8b3ae09f071c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Note: Replaced Item - 4DNESJC437VS", "status": "released", "aliases": ["static_header:replaced_item_4DNESJC437VS_by_4DNESNGESP28"], "options": {"filetype": "md", "title_icon": "info", "collapsible": false, "default_open": true}, "date_created": "2019-01-28T16:58:05.398299+00:00", "section_type": "Item Page Header", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-01-31T16:10:22.833517+00:00"}, "schema_version": "2", "@id": "/static-sections/96aee7a8-7ca3-45d6-9a7f-6cfb3e3d49ba/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "96aee7a8-7ca3-45d6-9a7f-6cfb3e3d49ba", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267111888"]}, "display_title": "Note: Replaced Item - 4DNESJC437VS", "external_references": [], "content": "This experiment set was replaced by [4DNESNGESP28](https://data.4dnucleome.org/experiment-set-replicates/4DNESNGESP28/) because new technical replicates were added.", "filetype": "md", "content_as_html": "<div class=\"markdown-container\"><p>This experiment set was replaced by <a href=\"https://data.4dnucleome.org/experiment-set-replicates/4DNESNGESP28/\" rel=\"noopener noreferrer\" target=\"_blank\">4DNESNGESP28</a> because new technical replicates were added.</p></div>"}], "project_release": "2018-07-06", "contributing_labs": [{"@id": "/labs/feng-yue-lab/", "status": "current", "display_title": "Feng Yue, PSU", "uuid": "6240db37-c902-4f2a-b8eb-44a3e6ccfe11", "@type": ["Lab", "Item"], "correspondence": [{"contact_email": "Znl1ZUBobWMucHN1LmVkdQ==", "@id": "/users/7c6184f0-3198-41d2-bb71-e7af0a9a74f0/", "display_title": "Feng Yue"}], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6240db37-c902-4f2a-b8eb-44a3e6ccfe11"]}}], "experiments_in_set": [{"files": [{"md5sum": "6c0a78f350735a19424e388327d92e98", "file_type_detailed": "reads (fastq)", "status": "archived", "uuid": "481454f2-e2ae-4dec-9d84-6420602ee527", "file_classification": "raw file", "upload_key": "481454f2-e2ae-4dec-9d84-6420602ee527/4DNFIHQ8L5W5.fastq.gz", "accession": "4DNFIHQ8L5W5", "display_title": "4DNFIHQ8L5W5.fastq.gz", "href": "/files-fastq/4DNFIHQ8L5W5/@@download/4DNFIHQ8L5W5.fastq.gz", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], 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UCSD"}, "lab": {"display_title": "Sheng Zhong, UCSD", "@id": "/labs/sheng-zhong-lab/", "uuid": "3452dfa5-ee8b-4dbc-8068-00cadde268b9", "name": "sheng-zhong-lab", "@type": ["Lab", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3452dfa5-ee8b-4dbc-8068-00cadde268b9"]}}, "related_files": [{"relationship_type": "paired with", "file": {"file_type_detailed": "reads (fastq)", "display_title": "4DNFIEWU4VLJ.fastq.gz", "@id": "/files-fastq/4DNFIEWU4VLJ/", "accession": "4DNFIEWU4VLJ", "uuid": "5c693443-07ad-4bfb-92ec-e7cf6a823a9d", "file_type": "reads", "status": "archived", "@type": ["FileFastq", "File", "Item"], "paired_end": "2", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "file_format": "fastq", "display_title": "fastq", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "file_format": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"md5sum": "b3803a23506b8c0820c7b07e4067f243", "file_type_detailed": "reads (fastq)", "status": "archived", "uuid": "5c693443-07ad-4bfb-92ec-e7cf6a823a9d", "file_classification": "raw file", "upload_key": "5c693443-07ad-4bfb-92ec-e7cf6a823a9d/4DNFIEWU4VLJ.fastq.gz", "accession": "4DNFIEWU4VLJ", "display_title": "4DNFIEWU4VLJ.fastq.gz", "href": "/files-fastq/4DNFIEWU4VLJ/@@download/4DNFIEWU4VLJ.fastq.gz", "file_type": "reads", "@type": ["FileFastq", "File", "Item"], "file_size": 1647489932, "paired_end": "2", 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