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Genome-wide resources of endoribonucleotide-prepared short interfering RNAs for specific loss-of-function studies

ABSTRACT: RNA interference (RNAi) has become an important technique for loss-of-gene functionstudies in mammalian cells. To achieve reliable results in an RNAi experiment, efficientand specific silencing triggers are required. Here we present genome-wide data sets forthe production of endoribonuclease-prepared short interfering RNAs (esiRNAs) for human, mouse and rat. We used an algorithm to predict the optimal region for esiRNA synthesis for every protein-coding gene of these three species. The database RiDDLE was installed for retrieval of target sequences and primer information. To test this in silico resource experimentally, we generated 16,242 esiRNAs that can be used for RNAi screening in human cells. Comparative analyses with chemically synthesized siRNAs demonstrated a high silencing efficacy of esiRNAs and a 12-fold reduction of downregulated off-target transcripts as detected by microarray analysis. Hence, the presented esiRNA libraries offer an efficient, cost-effective, and specific alternative to currently available mammalian RNAi resources. Consensus gene lists used to generate the clusters appearing in the associated publication have been linked as supplementary files at the foot of the Series record. There is a consensus genelist for each gene in the study: GSE6807_KIAA1387_ConsensusGeneList.txt GSE6807_MAPK14_ConsensusGeneList.txt Keywords: RNAi, off-target effects, esiRNA

ORGANISM(S): Homo sapiens

PROVIDER: GSE6807 | GEO | 2007/04/10

SECONDARY ACCESSION(S): PRJNA99211

REPOSITORIES: GEO

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