Short hairpin RNA databases | Non-coding transcript data analysis
Shortly after the cellular mechanism of RNA interference (RNAi) was first described, scientists began using this powerful technique to study gene function. This included designing better methods for the successful delivery of small interfering RNAs (siRNAs) and short hairpin RNAs (shRNAs) into mammalian cells. While the simplest method for RNAi is the cytosolic delivery of siRNA oligonucleotides, this technique is limited to cells capable of transfection and is primarily utilized during transient in vitro studies. The introduction of shRNA into mammalian cells through infection with viral vectors allows for stable integration of shRNA and long-term knockdown of the targeted gene; however, several challenges exist with the implementation of this technology.
A manually curated database of HIV inhibiting siRNAs that provides comprehensive information about each siRNA or shRNA. HIVsirDB structure contains sixteen fields including siRNA sequence, HIV strain, targeted genome region, efficacy and conservation of target sequences. Users can explore information in user friendly manner using the search and browsing facility. HIVsirDB is useful to experimentalists in deciding the highly potent siRNAs targeting the most susceptible target site in HIV genome and its experimental procedure to suppress HIV infection.
Gathers information about shRNA. COLT-Cancer is a web-accessible database system that assists users to explore shRNA activities. This platform contains several functions allowing to browse, query and analyze pooled shRNA screening data from a deep repository. Moreover, this resource permits identification of genetic vulnerabilities for cancer cell proliferation.
Allows researchers worldwide access to information as well as allow purchase of the constructs. RNAi Codex holds data from the Hannon–Elledge shRNA library and allows the use of biologist-friendly gene names to access information on shRNA constructs that can silence the gene of interest. It is designed to hold user-contributed annotations and publications for each construct, as and when such data become available.
Enables collaboration by establishing a centralized catalog of shRNA sequences. You can use it to manage lists of shRNA sequences owned by your lab, search for specific sequences owned by any lab, import sequence lists from CSV files, and to rate and comment on sequences with which you're familiar.