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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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RNAi knock down of endogenous genes and luciferase reporters in human HeLa cells to examine the effect of seed complement frequency on off-target signatures

ABSTRACT: siRNAs were designed against both endogenous genes and luciferase reporters to examine the effect of seed complement frequency on off-target signatures as measured by Agilent Human 1A gene expression analysis.

INSTRUMENT(S): G2505B DNA microarray scanner

ORGANISM(S): Homo sapiens

SUBMITTER: Emily Anderson

PROVIDER: E-MEXP-1402 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Experimental validation of the importance of seed complement frequency to siRNA specificity.

Anderson Emily M EM Birmingham Amanda A Baskerville Scott S Reynolds Angela A Maksimova Elena E Leake Devin D Fedorov Yuriy Y Karpilow Jon J Khvorova Anastasia A

RNA (New York, N.Y.) 20080326 5

Pairing between the hexamer seed region of a small interfering RNA (siRNA) guide strand (nucleotides 2-7) and complementary sequences in the 3' UTR of mature transcripts has been implicated as an important element in off-target gene regulation and false positive phenotypes. To better understand the association between seed sequences and off-target profiles we performed an analysis of all possible (4096) hexamers and identified a nonuniform distribution of hexamer frequencies across the 3' UTR tr ...[more]

PMID: 18367722

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