Frontiers in RNAi

RNA interference (RNAi) is a biological process in which small nucleotide sequences destroy specific mRNA molecules and, therefore, interrupt genetic expression. RNAi has rapidly developed into a ...
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Public Repositories for RNAi Screening Data

Pp. 40-57 (18)

Esther E. Schmidt, Michael S. Banos, Jennifer A. Smith, Amanda Birmingham, Michael Boutros and Caroline E. Shamu

Abstract

Public repositories for genomic data, such as sequencing and expression studies, play key roles in the dissemination of large-scale studies. It can be expected that repositories for functional genomic data, such as RNAi screens, will have a similar important role. RNAi data repositories store information about RNAi reagents and results from RNAi screening experiments, and present them in a structured and searchable manner. Implementation and use of robust, public RNAi databases is critical to realizing the potential of RNAi experiments. These databases allow investigators to re-analyze deposited datasets to ask new and different questions, and they are a rich source for functional gene annotation. This chapter describes challenges faced as databases for genome-scale RNAi screening results are developed: the diversity of RNAi assays carried out in multiple cell types and organisms; the variety of identifiers and annotations used to describe RNAi reagents; the lack of an established and accepted ontology to describe RNAi experiments; and the challenge of curating RNAi screening results and collecting complete datasets. Examples of Laboratory Information Management Systems (LIMS) that store RNAi data and of RNAi reagent and result annotation databases are provided.

Keywords:

Data annotation, data comparison, data curation, data management, data repository, database, genome-scale RNAi screen, high throughput screening (HTS), RNA interference, RNAi, shRNA, siRNA.RNA interference, RNAi, siRNA, shRNA, database, high throughput screening (HTS), data repository, data management, data comparison, data annotation, genome-scale RNAi screen, data curation

Affiliation:

German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany.