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https://www.encodeproject.org/
Consortium to build comprehensive parts list of functional elements in human genome. This includes elements that act at protein and RNA levels, and regulatory elements that control cells and circumstances in which gene is active. Data from 2012-present.
Proper citation: Encode (RRID:SCR_015482) Copy
Public research university in Santa Cruz, California. It is one of 10 campuses in the University of California system.
Proper citation: University of California at Santa Cruz; California; USA (RRID:SCR_011624) Copy
http://promoter.bx.psu.edu/hi-c/
Genome Browser for study of 3D genome organization and gene regulation and data visualization. Used to visualizing chromatin interaction data, browse other omics data such as ChIP-Seq or RNA-Seq for same genomic region, and gain complete view of both regulatory landscape and 3D genome structure for any given gene., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: 3D Genome (RRID:SCR_017525) Copy
A comprehensive encyclopedia of genomic functional elements in the model organisms C. elegans and D. melanogaster. modENCODE is run as a Research Network and the consortium is formed by 11 primary projects, divided between worm and fly, spanning the domains of gene structure, mRNA and ncRNA expression profiling, transcription factor binding sites, histone modifications and replacement, chromatin structure, DNA replication initiation and timing, and copy number variation. The raw and interpreted data from this project is vetted by a data coordinating center (DCC) to ensure consistency and completeness. The entire modENCODE data corpus is now available on the Amazon Web Services EC2 cloud. What this means is that virtual machines and virtual compute clusters that you run within the EC2 cloud can mount the modENCODE data set in whole or in part. Your software can run analyses against the data files directly without experiencing the long waits and logistics associated with copying the datasets over to your local hardware. You may also view the data using GBrowse, Dataset Search, or download the data via FTP, as well as download pre-release datasets.
Proper citation: modENCODE (RRID:SCR_006206) Copy
Private, non profit university in Stanford, California, USA for research and undergraduate and graduate studies. Known for its academic strength, wealth, proximity to Silicon Valley, and ranking as one of the world's top universities. Particularly noted for its entrepreneurship and is one of the most successful universities in attracting funding for start-ups.
Proper citation: Stanford University; Stanford; California (RRID:SCR_011538) Copy
Encyclopedia of DNA elements consisting of list of functional elements in human genome, including elements that act at protein and RNA levels, and regulatory elements that control cells and circumstances in which gene is active. Enables scientific and medical communities to interpret role of human genome in biology and disease. Provides identification of common cell types to facilitate integrative analysis and new experimental technologies based on high-throughput sequencing. Genome Browser containing ENCODE and Epigenomics Roadmap data. Data are available for entire human genome.
Proper citation: ENCODE (RRID:SCR_006793) Copy
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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