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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of human HeLa cells treated with various functional siRNAs to investigate RNAi off-targets

ABSTRACT: Human HeLa cells were treated with various functional siRNAs of different sequence targeting several genes (100 nM or 50 nM for 24 hours). There are two transfection groups - in the first, containing biological duplicates (A and B), the mock-transfected control samples are pooled as a Cy3 reference. The second group is a from a single transfection with each siRNA delivered at two concentrations (50 and 100 nM). A mock-to-untransfected and/or a mock-to-mock self array are control arrays for each group. These sample groups are designated as biological or functional (dose of 100 or 50 nM) duplicates, respectively, in the publication.

INSTRUMENT(S): G2505B DNA microarray scanner

ORGANISM(S): Homo sapiens

SUBMITTER: Emily Anderson

PROVIDER: E-MEXP-668 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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3' UTR seed matches, but not overall identity, are associated with RNAi off-targets.

Birmingham Amanda A Anderson Emily M EM Reynolds Angela A Ilsley-Tyree Diane D Leake Devin D Fedorov Yuriy Y Baskerville Scott S Maksimova Elena E Robinson Kathryn K Karpilow Jon J Marshall William S WS Khvorova Anastasia A

Nature methods 20060301 3

Off-target gene silencing can present a notable challenge in the interpretation of data from large-scale RNA interference (RNAi) screens. We performed a detailed analysis of off-targeted genes identified by expression profiling of human cells transfected with small interfering RNA (siRNA). Contrary to common assumption, analysis of the subsequent off-target gene database showed that overall identity makes little or no contribution to determining whether the expression of a particular gene will b ...[more]

PMID: 16489337

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