Project description:Changes in the cellular transcriptome, proteome and phosphorylated proteome after knockdown of ERK5 protein in HCT116 cells using PROTACs and siRNA, respectively.
Project description:Gene expression profiling comparisons of Neuro2a transfected with either mKIAA1583 (Tmem132a) siRNA or control (non-specific) siRNA. Keywords: siRNA, gene expression
Project description:A GAPDH siRNA was overexpressed in HeLa cells and microarray expression profiling was performed to experimentally identify the off-targets of this siRNA at the transcriptome level. Among all predicted siRNA off-targets by MirTarget2, the majority were downregulated by at least 10% (i.e. less than 90% remaining gene expression). Moreover, more than one fifth were downregulated by at least 30%. The gene knockdown data is consistent with previous observations that siRNA off-targets are generally silenced at a more moderate level as compared to silencing of the single intended target
Project description:To examine the role of NRF2 in accelerating cell proliferation and to identify the target genes responsible for this function, transcriptome analysis was performed using A549 cells, in which NRF2 is constitutively activated. NRF2 was knocked down by siRNA against NRF2, and the gene expression profile was compared with that of A549 cells treated with control siRNA. To exclude off-target effects, three different siRNAs against NRF2 was independently applied.
Project description:Short interfering RNAs (siRNA) are widely used as tool for gene inactivation in basic research and therapeutic applications. One of the major shortcomings of siRNA experiments are sequence-specific Off-target effects. Such effects are largely unpredictable because siRNAs can affect partially complementary sequences and function like microRNAs (miRNAs), which inhibit gene expression on mRNA stability or translational levels. Here we demonstrate that novel, enzymatically generated siRNA pools - referred to as siPools - containing up to 60 accurately defined siRNAs eliminate Off-target effects. This is achieved by the low concentration of each individual siRNA diluting sequence-specific Off-target effects below detection limits. In fact, whole transcriptome analyses reveal that single siRNA transfections can severely affect global gene expression. However, when complex siRNA pools are transfected, almost no transcriptome alterations are observed. Taken together, we present enzymatically-produced complex but accurately defined siRNA pools with potent On-target silencing but without detectable Off-target effects.
Project description:To clarify the effect of SHP in LXRs-mediated signaling pathway, we performed global gene expression analysis of SHP siRNA transfected- or control siRNA transfected- astrocytes after IFN-γ and LXRs agonist. Microarray analysis revealed that expression of several genes encoding inflammatory mediators were reversed in SHP siRNA transfected-astrocytes, when compared with control siRNA transfected-astrocytes.
Project description:We compared the transcriptome of four human PDA lines: HPAF-II, Panc.05.04, Panc.8 and Panc.10.05 transfected with control siRNA or Pdx1 siRNA.
