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E-GEOD-28786 - siRNA off-target effects can be reduced at concentrations that match their individual potency

Status
Released on 31 July 2011, last updated on 16 August 2011
Organism
Homo sapiens
Samples (54)
Array (1)
Protocols (6)
Description
This study demonstrates that siRNA off-targets (e.g. 3'UTR off-targets), can be significantly reduced when cells are treated with a relatively low dose of siRNA (e.g. 1nM) that is sufficient to effectively silence the intended target. Cells were treated with different concentrations of either unmodified siRNA or modified siRNA that targeted either hexokinase2 or STAT3 (HK2-3581, HK2-4031, HK2-3581M, STAT3-1676, STAT3-1676M). As transfection efficiencies can vary according to the ratio of nucleotide to transfection reagent, each dose was supplemented with non-targeting/negative control siRNA (siGenome2 or Allstars negative control), such that the total RNA concentration was equal across experiments. RNA was purified 48 hours post-transfection using the RNeasy mini kit from Qiagen. Biological replicates were normalized using the RMA method and analyzed using various Bioconductor tools.
Experiment type
transcription profiling by array 
Contacts
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-28786.idf.txt
Sample and data relationshipE-GEOD-28786.sdrf.txt
Raw data (2)E-GEOD-28786.raw.1.zip, E-GEOD-28786.raw.2.zip
Processed data (1)E-GEOD-28786.processed.1.zip
Array designA-GEOD-9324.adf.txt
R ExpressionSetE-GEOD-28786.eSet.r
Links