{"lab": {"display_title": "Mitchell Guttman, CALTECH", "@id": "/labs/mitchell-guttman-lab/", "status": "current", "correspondence": [{"contact_email": "bWd1dHRtYW5AY2FsdGVjaC5lZHU=", "@id": "/users/ac3920c8-caa6-444b-be8a-48b52a1dcb3e/", "display_title": "Mitchell Guttman"}], "@type": ["Lab", "Item"], "title": "Mitchell Guttman, CALTECH", "uuid": "c17e88b5-912a-496a-acc7-28dd71215a7d", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.c17e88b5-912a-496a-acc7-28dd71215a7d"]}}, "award": {"center_title": "NBC - Guttman", "@id": "/awards/1U01DA040612-01/", "name": "1U01DA040612-01", "uuid": "4de1cf81-1ea0-4a19-bc7a-dd3343b34438", "status": "current", "display_title": "DECIPHERING THE FUNCTION AND MECHANISMS OF LNCRNA-MEDIATED ORGANIZATION OF NUCLEAR COMPARTMENTS", "project": "4DN", "@type": ["Award", "Item"], "description": "NBC: The nucleus of each cell is a complex arrangement of DNA, RNA, and protein that is dynamically organized into various nuclear bodies and compartments that are often arranged around shared functional and regulatory roles. Yet, while many of these nuclear compartments were first identified several decades ago a major challenge with characterizing these compartments is that there are currently no biochemical methods for isolating individual nuclear compartments. Importantly, many nuclear bodies are marked and maintained by nuclear retained long non-coding RNAs (lncRNAs). Here we aim to develop several novel technologies to purify the molecular constituents of nuclear domains and their necessity and sufficiency in forming these compartments. Together these technologies will allow us to systematically address the following questions: Aim 1: What are the optimal biochemical conditions in which to specifically and accurately purify specific nuclear bodies and compartments in order to identify their DNA, RNA and protein components? A critical aspect of biochemical purifications is the fine balance between cross-linking conditions that identify direct molecular interactions while not over-crosslinking that could result in indirect interactions. Usin known nuclear compartments such as the nucleolus, nuclear speckles, and paraspeckles we will optimize RAP for isolating DNA-RNA, RNA-RNA, RNA-protein interactions. We aim to identify universally applicable purification conditions to identify molecular interactions within nuclear and other subcellular structures. Aim 2: What are the DNA, RNA and protein factors involved in nuclear compartments? Although most known nuclear bodies are characterized by lncRNAs the other RNA, DNA and protein factors remain less well defined. Here we will develop technologies to catalog the molecular factors that comprise various nuclear bodies. We will further validate these components through colocalization of these components within a nuclear domain using visualization approaches (e.g. RNA-DNA Co-FISH). Overall we aim to apply new technologies to systematic and comprehensive catalog of RNA, DNA and Proteins in nuclear bodies. Aim 3: Are lncRNAs and proteins necessary and/or sufficient for nuclear compartmentalization? Here we will develop a novel technology platform, termed CRISPR-Display, which allows long RNA cargos to be appended and delivered by CRISPR-Cas9 systems to a desired site in the genome. We will develop this technology to test if lncRNA molecules are sufficient to drive nuclear organization. We will also use CRISPR-Display to multiplex several RNA aptamers that can be used to recruit proteins (with reciprocal protein epitopes that bind RNA aptamers) and test if they are sufficient to form nuclear compartments. In parallel we will perform loss-of- function approaches to identify protein and or RNA components are required for establishing nuclear domains. Collectively our proposal aims to develop powerful and multifaceted technologies to catalog the molecular components of subnuclear structures, validate these interactions and test their biological importance.", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "badges": [{"badge": {"title": "Biosample Metadata Incomplete", "badge_icon": "/static/img/badges/biosample-icon.svg", "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"], "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "warning": "Biosample Metadata Incomplete", "badge_classification": "Warning", "@id": "/badges/biosample-metadata-incomplete/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "messages": ["Biosample missing doubling_number", "Biosample missing passage_number", "Biosample missing culture_duration", "Biosample missing morphology_image", "Biosample is a stem cell line with unknown passage number missing karyotype"]}], "status": "released", "aliases": ["mitchell-guttman-lab:SAMN09257734"], "dbxrefs": ["BioSample:SAMN09257734"], "accession": "4DNBSAPE2VOP", "biosource": [{"lab": {"status": "current", "uuid": "c17e88b5-912a-496a-acc7-28dd71215a7d", "display_title": "Mitchell Guttman, CALTECH", "@type": ["Lab", "Item"], "@id": "/labs/mitchell-guttman-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.c17e88b5-912a-496a-acc7-28dd71215a7d"]}}, "award": {"uuid": "4de1cf81-1ea0-4a19-bc7a-dd3343b34438", "display_title": "DECIPHERING THE FUNCTION AND MECHANISMS OF LNCRNA-MEDIATED ORGANIZATION OF NUCLEAR COMPARTMENTS", "@type": ["Award", "Item"], "status": "current", "@id": "/awards/1U01DA040612-01/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "tissue": {"uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "term_url": "http://purl.obolibrary.org/obo/CL_0000034", "preferred_name": "stem cell", "synonyms": ["animal stem cell"], "@id": "/ontology-terms/CL:0000034/", "term_id": "CL:0000034", "status": "released", "display_title": "stem cell", "term_name": "stem cell", "@type": ["OntologyTerm", "Item"], "slim_terms": [{"status": "current", "term_url": "http://purl.obolibrary.org/obo/GO_0005623", "term_name": "cell", "term_id": "GO:0005623", "preferred_name": "cell", "display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "term_url": "http://purl.obolibrary.org/obo/CL_0000000", "term_name": "cell", "term_id": "CL:0000000", "preferred_name": "cell", "display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "aliases": ["mitchell-guttman-lab:pSM33"], "accession": "4DNSR75M6LKH", "cell_line": {"preferred_name": "pSM33", "display_title": "pSM33", "term_id": "4DN:0000261", "@type": ["OntologyTerm", "Item"], "term_name": "pSM33", "status": "released", "@id": "/ontology-terms/4DN:0000261/", "uuid": "ff4ce5bf-9af3-40ed-8d94-17dd1c91910c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"status": "released", "@id": "/individuals-mouse/4DNIN7XXG421/", "sex": "male", "uuid": "24156d76-370c-4ef8-9308-809426033187", "display_title": "4DNIN7XXG421", "@type": ["IndividualMouse", "Individual", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "description": "A male embryonic stem cell line with a dox-inducible Xist gene.", "date_created": "2018-11-15T18:08:17.798061+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-09-19T19:54:39.259739+00:00"}, "modifications": [{"@type": ["Modification", "Item"], "uuid": "2fb4dbc8-941f-4b3f-bf28-ef5841428346", "display_title": "insertion of Tet-On activator M2rtTA at ROSA26", "status": "released", "@id": "/modifications/2fb4dbc8-941f-4b3f-bf28-ef5841428346/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["Modification", "Item"], "uuid": "dc038463-4ae8-472c-91aa-b6b472ed4a0c", "display_title": "targeted integration of Xist with dox-inducible promoter", "status": "released", "@id": "/modifications/dc038463-4ae8-472c-91aa-b6b472ed4a0c/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "biosource_type": "stem cell derived cell line", "cell_line_tier": "Unclassified", "public_release": "2018-12-03", "schema_version": "2", "project_release": "2018-12-03", "@id": "/biosources/4DNSR75M6LKH/", "@type": ["Biosource", "Item"], "uuid": "aff65913-920d-4d7c-a051-77f2e399037f", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "pSM33 with insertion of Tet-On activator M2rtTA at ROSA26, targeted integration of Xist with dox-inducible promoter - 4DNSR75M6LKH", "external_references": [], "biosource_name": "pSM33 with insertion of Tet-On activator M2rtTA at ROSA26, targeted integration of Xist with dox-inducible promoter", "biosource_category": ["Mouse stem cell"], "organism": {"uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "name": "mouse", "status": "released", "@id": "/organisms/10090/", "display_title": "M. musculus", "@type": ["Organism", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "treatments": [{"status": "released", "chemical": "doxycycline", "duration": 24.0, "@type": ["TreatmentAgent", "Treatment", "Item"], "@id": "/treatments-agent/6e4e384f-3702-4939-8d2f-5bf096169f01/", "treatment_type": "Chemical", "uuid": "6e4e384f-3702-4939-8d2f-5bf096169f01", "concentration_units": "\u03bcg/mL", "duration_units": "hour", "concentration": 2.0, "display_title": "doxycycline treatment (2.0 \u03bcg/mL, 24.0h at 37.0\u00b0C)", "temperature": 37.0, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "description": "pSM33 biosample", "date_created": "2018-11-15T18:08:21.669242+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-05-09T14:11:29.713502+00:00"}, "public_release": "2018-12-03", "schema_version": "2", "project_release": "2018-12-03", "cell_culture_details": [{"lab": {"uuid": "c17e88b5-912a-496a-acc7-28dd71215a7d", "display_title": "Mitchell Guttman, CALTECH", "status": "current", "@id": "/labs/mitchell-guttman-lab/", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.c17e88b5-912a-496a-acc7-28dd71215a7d"]}}, "award": {"uuid": "4de1cf81-1ea0-4a19-bc7a-dd3343b34438", "status": "current", "@id": "/awards/1U01DA040612-01/", "display_title": "DECIPHERING THE FUNCTION AND MECHANISMS OF LNCRNA-MEDIATED ORGANIZATION OF NUCLEAR COMPARTMENTS", "@type": ["Award", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "aliases": ["mitchell-guttman-lab:SAMN09257734-cellculture"], "description": "Female hybrid mouse ES cell lines were cultured in serum-free 2i/LIF medium and maintained at an exponential growth phase. We induced Xist expression in these cells using doxycycline (Sigma, D9891) at a final concentration of 2ug/ml for 24hrs.", "date_created": "2018-11-15T18:08:19.056821+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2018-12-03T20:19:33.109382+00:00"}, "public_release": "2018-12-03", "schema_version": "2", "project_release": "2018-12-03", "culture_start_date": "2016-05-25", "culture_harvest_date": "2016-06-21", "@id": "/biosample-cell-cultures/d0d7acae-d18c-4224-953f-9b9b953dd6bb/", "@type": ["BiosampleCellCulture", "Item"], "uuid": "d0d7acae-d18c-4224-953f-9b9b953dd6bb", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "BiosampleCellCulture from 2018-11-15", "external_references": []}], "@id": "/biosamples/4DNBSAPE2VOP/", "@type": ["Biosample", "Item"], "uuid": "36a50c39-92e8-461f-8a89-86300925a089", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNBSAPE2VOP", "external_references": [{"ref": "BioSample:SAMN09257734", "uri": "https://www.ncbi.nlm.nih.gov/biosample/SAMN09257734"}], "modifications_summary": "None", "modifications_summary_short": "None", "treatments_summary": "doxycycline treatment (2.0 \u03bcg/mL, 24.0h at 37.0\u00b0C)", "tissue_organ_info": {"tissue_source": "stem cell"}, "biosource_summary": "pSM33 with insertion of Tet-On activator M2rtTA at ROSA26, targeted integration of Xist with dox-inducible promoter", "biosample_type": "stem cells", "biosample_category": ["Mouse stem cell"], "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSAPE2VOP/", "embedded_path": "badges", "item": {"messages": ["Biosample missing doubling_number", "Biosample missing passage_number", "Biosample missing culture_duration", "Biosample missing morphology_image", "Biosample is a stem cell line with unknown passage number 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": []}