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E-GEOD-14434 - Platform comparison of U1 Adaptors - a new gene silencing technology vs. siRNA

Status
Submitted on 14 January 2009, released on 21 February 2009, last updated on 1 May 2014
Organism
Homo sapiens
Samples (3)
Array (1)
Protocols (6)
Description
The goal of the microarray experiment was to do a head-to-head comparison of the U1 Adaptor technology with siRNA in terms of specificity at the genome-wide level. U1 Adaptors represent a novel gene silencing method that employs a mechanism of action distinct from antisense and RNA interference (RNAi). The U1 Adaptor is a bifunctional oligonucleotide having a “Target Domain” that is complementary to a site in the target gene's terminal exon and a “U1 Domain” that binds to the U1 small nuclear RNA (snRNA) component of the U1 small nuclear ribonucleoprotein (U1 snRNP) splicing factor. Tethering of U1 snRNP to the target pre-mRNA inhibits 3' end processing (i.e., polyA tail addition) leading to degradation of that RNA species within the nucleus thereby reducing mRNA levels. We demonstrate that U1 Adaptors can specifically inhibit both reporter and endogenous genes. Further, targeting the same gene either with multiple U1 Adaptors or with U1 Adaptors and small interfering RNAs (siRNAs), strongly enhances gene silencing, the latter as predicted from their distinct mechanisms of action. Such combinatorial targeting requires lower amounts of oligonucleotides to achieve potent silencing. Experiment Overall Design: For each sample total RNA was prepared from 3 independent transfections and then were pooled and analyzed by QPCR and also by microarray.
Experiment types
other, unknown experiment type
Contact
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-14434.idf.txt
Sample and data relationshipE-GEOD-14434.sdrf.txt
Raw data (1)E-GEOD-14434.raw.1.zip
Processed data (1)E-GEOD-14434.processed.1.zip
Array designA-AFFY-44.adf.txt
R ExpressionSetE-GEOD-14434.eSet.r
Links