Eurie L Hong | Search bioRxiv

bioRxiv2016

SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata

The Encyclopedia of DNA elements (ENCODE) project is an ongoing collaborative effort[1-6] to create a comprehensive catalog of functional elements initiated shortly after the completion of the Human Genome Project[7][1]. The current database exceeds 6500 experiments across more than 450 cell lines and tissues using a wide array of experimental techniques to study the chromatin structure, regulatory and transcriptional landscape of the H. sapiens and M. musculus genomes. All ENCODE experimental data, metadata, and associated computational analyses are submitted to the ENCODE Data Coordination Center (DCC) for validation, tracking, storage, unified processing, and distribution to community resources and the scientific community. As the volume of data increases, the identification and organization of experimental details becomes increasingly intricate and demands careful curation. The ENCODE DCC[8-10] has created a general purpose software system, known as SnoVault, that supports metadata and file submission, a database used for metadata storage, web pages for displaying the metadata and a robust API for querying the metadata. The software is fully open-source, code and installation instructions can be found at: http://github.com/ENCODE-DCC/snovault/ (for the generic database) and http://github.com/ENCODE-DCC/encoded/ to store genomic data in the manner of ENCODE. The core database engine, SnoVault (which is completely independent of ENCODE, genomic data, or bioinformatic data) has been released as a separate Python package.\n\nDatabase URL: https://www.encodeproject.org/

Bioinformatics↗

bioRxiv2015

Resources for the comprehensive discovery of functional RNA elements

Transcriptome-wide maps of RNA binding protein (RBP)-RNA interactions by immunoprecipitation (IP)-based methods such as RNA IP (RIP) and crosslinking and IP (CLIP) are key starting points for evaluating the molecular roles of the thousands of human RBPs. A significant bottleneck to the application of these methods in diverse cell-lines, tissues and developmental stages, is the availability of validated IP-quality antibodies. Using IP followed by immunoblot assays, we have developed a validated repository of 438 commercially available antibodies that interrogate 365 unique RBPs. In parallel, 362 short-hairpin RNA (shRNA) constructs against 276 unique RBPs were also used to confirm specificity of these antibodies. These antibodies can characterize subcellular RBP localization. With the burgeoning interest in the roles of RBPs in cancer, neurobiology and development, these resources are invaluable to the broad scientific community. Detailed information about these resources is publicly available at the ENCODE portal (https://www.encodeproject.org/).\n\nHighlightsO_LIAntibodies against 365 unique RBPs successfully immunoprecipitate the RBPs\nC_LIO_LIShort-hairpin RNAs against 276 unique RBPs confirm the specificity of RBP antibodies\nC_LIO_LIAntibodies characterize subcellular localization of RBPs\nC_LIO_LIAntibody and hairpin RNA information are provided at https://www.encodeproject.org/\nC_LI

Genomics↗