{"ID": "doi:10.1093/cercor/bhs015", "lab": {"display_title": "4DN DCIC, HMS", "@id": "/labs/4dn-dcic-lab/", "correspondence": [{"contact_email": "YW5kcmV3X3NjaHJvZWRlckBobXMuaGFydmFyZC5lZHU=", "@id": "/users/986b362f-4eb6-4a9c-8173-3ab267227777/", "display_title": "Andy Schroeder"}, {"contact_email": "YW5kcmVhX2Nvc29sb0BobXMuaGFydmFyZC5lZHU=", "@id": "/users/e4a22298-1da4-4e59-8a65-9e661f47fb48/", "display_title": "Andrea Cosolo"}, {"contact_email": "c2FyYWhfcmVpZmZAaG1zLmhhcnZhcmQuZWR1", "@id": "/users/e2324f87-0625-4bbc-803b-d47677aebe08/", "display_title": "Sarah Reiff"}], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "status": "current", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "url": "https://www.ncbi.nlm.nih.gov/pubmed/22368089", "award": {"display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER", "@id": "/awards/1U01CA200059-01/", "project": "4DN", "description": "DCIC: The goals of the 4D Nucleome (4DN) Data Coordination and Integration Center (DCIC) are to collect, store, curate, display, and analyze data generated in the 4DN Network. We have assembled a team of investigators with a strong track record in analysis of chromatin interaction data, image processing and three-dimensional data visualization, integrative analysis of genomic and epigenomic data, data portal development, large-scale computing, and development of secure and flexible cloud technologies. In Aim 1, we will develop efficient submission pipelines for data and metadata from 4DN data production groups. We will define data/metadata requirements and quality metrics in conjunction with the production groups and ensure that high-quality, well- annotated data become available to the wider scientific community in a timely manner. In Aim 2, we will develop a user-friendly data portal for the broad scientific community. This portal will provide an easy-to-navigate interface for accessing raw and intermediate data files, allow for programmatic access via APIs, and will incorporate novel analysis and visualization tools developed by DCIC as well as other Network members. For computing and storage scalability and cost-effectiveness, significant efforts will be devoted to development and deployment of cloud-based technology. We will conduct tutorials and workshops to facilitate the use of 4DN data and tools by external investigators. In Aim 3, we will coordinate and assist in conducting integrative analysis of the multiple data types. These efforts will examine key questions in higher-order chromatin organization using both sequence and image data, and the tools and algorithms developed here will be incorporated into the data portal for use by other investigators. These three aims will ensure that the data generated in 4DN will have maximal impact for the scientific community.", "@type": ["Award", "Item"], "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "status": "current", "name": "1U01CA200059-01", "center_title": "DCIC - DCIC", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "The development and activity-dependent expression of aggrecan in the cat visual cortex.", "status": "current", "authors": ["Kind PC", "Sengpiel F", "Beaver CJ", "Crocker-Buque A", "Kelly GM", "Matthews RT", "Mitchell DE"], "journal": "Cerebral cortex (New York, N.Y. : 1991)", "abstract": "The Cat-301 monoclonal antibody identifies aggrecan, a chondroitin sulfate proteoglycan in the cat visual cortex and dorsal lateral geniculate nucleus (dLGN). During development, aggrecan expression increases in the dLGN with a time course that matches the decline in plasticity. Moreover, examination of tissue from selectively visually deprived cats shows that expression is activity dependent, suggesting a role for aggrecan in the termination of the sensitive period. Here, we demonstrate for the first time that the onset of aggrecan expression in area 17 also correlates with the decline in experience-dependent plasticity in visual cortex and that this expression is experience dependent. Dark rearing until 15 weeks of age dramatically reduced the density of aggrecan-positive neurons in the extragranular layers, but not in layer IV. This  effect was reversible as dark-reared animals that were subsequently exposed to light showed normal numbers of Cat-301-positive cells. The reduction in aggrecan  following certain early deprivation regimens is the first biochemical correlate of the functional changes to the gamma-aminobutyric acidergic system that have been reported following early deprivation in cats.", "categories": ["integrative analysis"], "date_created": "2022-08-10T16:08:29.026361+00:00", "published_by": "External", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2022-08-10T16:09:28.894349+00:00"}, "date_published": "2013-02", "public_release": "2022-08-10", "schema_version": "2", "static_content": [{"content": {"error": "no view permissions"}, "location": "header"}, {"content": {"description": "Two BigWig tracks plus annotations for gene GRCm38 (tileset 'IUcqX4GzTNWJIzE2-b_sZg') and chromosome 'Z_YbBZW9RAq5V1oKvvp3hg'.", "display_title": "Test BigWig Display", "filetype": "HiglassViewConfig", "status": "released", "title": "Test BigWig Display", "@id": "/higlass-view-configs/00000000-1111-0000-1111-000000000001/", "name": "00000000-1111-0000-1111-000000000001", "award": {"@id": "/awards/1U01CA200059-01/", "status": "current", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER", "@type": ["Award", "Item"], "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["HiglassViewConfig", "UserContent", "Item"], "uuid": "00000000-1111-0000-1111-000000000001", "lab": {"status": "current", "@type": ["Lab", "Item"], "display_title": "4DN DCIC, HMS", "@id": "/labs/4dn-dcic-lab/", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267307e3a"]}}, "location": "tab:summary", "description": "Figure 1: This is a figure."}], "project_release": "2022-08-10", "@id": "/publications/52e85c70-fe2d-11e3-9191-0800200c9a67/", "@type": ["Publication", "Item"], "uuid": "52e85c70-fe2d-11e3-9191-0800200c9a67", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "Kind PC et al. (2013) doi:10.1093/cercor/bhs015", "external_references": [], "short_attribution": "Kind PC et al. (2013)", "@context": "/terms/", "aggregated-items": {}, "validation-errors": []}