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Global analysis of off-target genes by GAPDH siRNA

ABSTRACT: 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

ORGANISM(S): Homo sapiens

PROVIDER: GSE41924 | GEO | 2013/10/03

SECONDARY ACCESSION(S): PRJNA178530

REPOSITORIES: GEO

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Global analysis of off-target genes by GAPDH siRNA

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 GAPDH siRNA was transfected into HeLa cells, and the unintended off-targets was identified by microarrays 24 hours post transfection.

2013-10-03 | E-GEOD-41924 | biostudies-arrayexpress

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

2011-08-01 | GSE28786 | GEO

Gene profile in H1299 cells treated with PTD-DRBD GAPDH siRNA or treated with Lipofection GAPDH siRNA

Project description:Whole genome microarrays were probed with total mRNA from PTD-DRBD GAPDH siRNA treated H1299 cells at 12 h and 24 h. Using a 1.6x fold increase/decrease filter of cellular mRNAs, we detected a dramatic reduction in the target GAPDH mRNA along with a limited number of both up and down regulated genes. The up regulated genes were reduced in numbers and to nearly background 1.6x levels at 24 h, while the down regulated genes increased slightly in numbers and maintained a similar magnitude at 24 h. In contrast, lipofection treated cells showed both a dramatic increase in both the total number of genes altered and the magnitude of the increase. In addition, the numbers of genes affected increased between 12 h and 24 h, suggesting that lipofection of siRNAs into cells results in a substantial alteration to the transcriptome and may thereby confound interpretation of experimental outcomes. Moreover, the GAPDH specific knockdown was significantly smaller than PTD-DRBD mediated knockdown. Total RNA obtained from H1299 cells treated with PTD-DRBD GAPDH siRNA, Lipofection GAPDH siRNA or PBS (Control) after 12 or 24 hours post-treatment

2010-05-08 | E-GEOD-15723 | biostudies-arrayexpress

Gene profile in H1299 cells treated with PTD-DRBD GAPDH siRNA or treated with Lipofection GAPDH siRNA

2009-05-22 | GSE15723 | GEO

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

Project 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.

2011-07-31 | E-GEOD-28786 | biostudies-arrayexpress

Comparison of STEEL siRNA-treated and control siRNA-treated human endothelial cells

Project description:To determine the role of STEEL in endothelial cell (EC) gene regulation, gene expression analysis was conducted on control and STEEL siRNA-treated human dermal microvascular endothelial cells (HMVECs) and human umbilical vein endothelial cells (HUVECs). A total of 225 protein-coding genes were downregulated and 80 were upregulated when both EC types were grouped for analysis. In HMVEC alone, 544 protein-coding genes were downregulated and 218 were upregulated. In HUVEC alone, 177 protein-coding genes were downregulated and 125 were upregulated. Prominently, STEEL siRNA depletion results in the downregulation of two notable protein-coding genes, eNOS and KLF2, which are modulated in ECs subjected to continuous laminar shear stress.

2018-03-30 | GSE108262 | GEO

Homo sapiens

Project description:Gene profile in H1299 cells treated with PTD-DRBD GAPDH siRNA or treated with Lipofection GAPDH siRNA

| PRJNA116613 | ENA

Full gene expression of pancreatic rat β-cell - RIN-m line treated with Edem2 siRNA

Project description:Non-treated, scrambled siRNA (control) and downregulated Edem2 samples were subjected to full gene expression. Ambion® Silencer® Select Pre-designed for rat Edem2 specific small interfering (siRNA) (cat. n. 4390771) and control (siSCR) (cat. n. 4390843) were purchased from (ThermoFisher). Lipofectamine® 2000 was used for transfecting siRNA in Opti-MEM™ Medium according to the manufacturer’s instruction. Edem2 mRNA level at 72 hours post-transfection was suppressed to 7.7% in siRNA cells compared to scrambled cells. The aim of this was to see the expression different when Edem2 was suppressed in normal condition.

2020-07-01 | E-MTAB-7583 | biostudies-arrayexpress

siRna

Project description:siRna Transcriptome or Gene expression

| PRJNA308857 | ENA

siRNA profiling of human primary prostate stromal cells knocked down for FOXF2

Project description:To identify the genes and pathways regulated by FOXF2, we investigated potential FOXF2 gene targets by microarray analyses of primary prostate stromal cells (PrSC) in which FOXF2 was knocked down by siRNA. 190 differentially expressed genes were selected, of which 104 genes were more highly expressed in PrSC cells treated with FOXF2 siRNA and 86 were more highly expressed in PRSC cells treated with negative control siRNA. Experiment Overall Design: In each experiment, we compared gene expression of PrSC cells treated with FOXF2 siRNA versus PrSC cells treated with negative control siRNA, in a total of 6 affymetrix arrays. 190 differentially expressed genes were selected (ratio negative control siRNA/siRNA â¥ 2log |0.8| as average in all arrays).

2008-11-13 | E-GEOD-12444 | biostudies-arrayexpress

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