Computational protocol: siRNA Off-Target Effects Can Be Reduced at Concentrations That Match Their Individual Potency

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Protocol publication

[…] Off-targets were assessed using the Affymetrix gene expression platform and all data is MIAME compliant and available at GEO (GSE28786). Biological triplicates were used unless specifically stated. RNA was hybridized to Affymetrix human genome U133 plus 2.0 arrays. The arrays were scanned using an Affymetrix GeneChip Scanner 3000. Probesets were mapped to Entrez Gene IDs using custom CDF files . Affymetrix CEL files were normalized in Bioconductor using the RMA method . Differentially regulated genes were identified using a moderated t-test . False discovery rate adjusted P-values were calculated using the method of Benjamini and Hochberg . Genes were mapped to GO terms using the AnnotationDbi package and GO enrichment analysis was performed using the GOstats package . The longest 3′UTR sequence for each human gene was retrieved using the ENSEMBL API and k-mer enrichment analysis was performed using an implementation of the Sylamer method . […]

Pipeline specifications

Software tools AnnotationDbi, GOstats, Sylamer
Application Genome annotation