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Optimized siRNAs with a minimal off-target effect facilitate the screening of essential genes in cancer cells

ABSTRACT: siRNAs with dN are a promising and easy approach to characterize essential genes by minimizing the off-target effect in cancer cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE62968 | GEO | 2015/07/01

SECONDARY ACCESSION(S): PRJNA266318

REPOSITORIES: GEO

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Optimized siRNAs with a minimal off-target effect facilitate the screening of essential genes in cancer cells

Project description:siRNAs with dN are a promising and easy approach to characterize essential genes by minimizing the off-target effect in cancer cells. mRNA profiles of HCT 116 cells after the transfection of siRNAs or blank control by deep sequencing, using HiSeq 2000

2015-07-01 | E-GEOD-62968 | biostudies-arrayexpress

siRNAs with decreased off-target effect facilitate the identification of essential genes in cancer cells.

Project description:Since the essential genes are crucial to the proliferation and survival of cancer cells, the interference of these genes is promising to be an option for cancer therapy to overcome heterogeneity. However, the essential genes are highly overestimated by RNA interference (RNAi) screenings, which is mainly caused by the pervasive off-target effect of small interference RNA (siRNA) and short hairpin RNA (shRNA). In the present study, we designed Match-Mismatch paired siRNAs to discriminate the on-target effect from off-target effect of siRNAs on cell viability. Only one of the 7 potential essential genes was validated as essential to cell viability, which demonstrates the high false positive rate in RNAi screenings. We modified the siRNA by introducing random nucleotides (N) into the guide strand to mitigate the off-target effect, without significantly compromising the on-target effect. The whole transcriptome profile analysis of cells transfected with siRNAs with or without Nindicates that siRNA-dN (with Ns on both the 2nd and the 18th bases of the guide strand) weakens the off-target effect by decreasing the unintended targets. The optimized siRNAs can be applied in the characterization of essential genes in cancer cells.

| S-EPMC4673289 | biostudies-literature

Transcription profiling by array of embryonic chick retina treated with Hes5.3 siRNAs, Atoh7 siRNAs and non-targeting siRNAs.

Project description:Transcription profiling by array of embryonic chick retina treated with Hes5.3 siRNAs, Atoh7 siRNAs and non-targeting siRNAs.

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Transcription profiling by array of embryonic chick retina treated with Hes5.3 siRNAs, Atoh7 siRNAs and non-targeting siRNAs.

Project description:The microarray analysis was designed to test the effects of Hes5.3 siRNAs, Atoh7 siRNAs and non-targeting siRNAs on gene expression at the periphery of the expanding Hes5.3 domain in embryonic chick retina. For this microarray we collected retina samples 16 hours after electroporation to complete our previous analysis performed on samples collected 36 hours after RNA interference treatment (Chiodini et al., 2013).

2020-08-01 | GSE147258 | GEO

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Project description:RPE-1 cells treated with the indicated siRNAs for 48 h were subjected to the tandem mass tag quantitative proteomics analysis.Carry out relative protein quantification analysis using tandem mass tag mass spectrometry in RPE-1 cells to investigate the mechanism underlying PCIF1 attenuates ciliation.

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Project description:We analyzed the C. elegans small RNA response to high copy transgene sequences expressed in the soma in a wild type and an eri-6/7 mutant background. We also analyzed small RNA defects in the arl-8(tm2472) mutant. Transgene siRNAs are 22 nt long, mostly antisense, and correspond to the promoter, coding regions, the 3'UTR and plamsid sequences present on the transgene. Transgene siRNAs are decreased in the eri-6/7 mutant. In the arl-8 mutant, 26G siRNAs in the ALG-3/4 dependent endogenous RNAi pathway are decreased.

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Selection of well-tolerated GalNAc-conjugated siRNAs by screening for RNAi-mediated off-target effects in rodent toxicity studies

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2018-01-11 | GSE108823 | GEO

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Optimized minimal genome-wide human sgRNA library

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2023-07-18 | GSE223086 | GEO

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