Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

SiPools: highly complex but accurately defined siRNA pools eliminate Off-target effects (HuGene-2_0)

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE57646 | GEO | 2014/05/15

SECONDARY ACCESSION(S): PRJNA247557

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

siPools: highly complex but accurately defined siRNA pools eliminate Off-target effects (HuGene-1_0 ENST)

2014-05-15 | GSE57667 | GEO

siPools: highly complex but accurately defined siRNA pools eliminate Off-target effects (HuGene-1_0 ENST)

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. To demonstrate the reduction of Off-target gene deregulation by use of complex siRNA pools (siPools), a single siRNA targeting human SCYL1 was transfected alone or in combination with 14 or 59 other siRNAs at a total siRNA concentration of 3 nM in human Hela cells. Mock transfected cells served as negative control. Every sample was tested in biological triplicates. Total RNA was extract 48h after transfection for affimetrix expression analysis.

2014-05-15 | E-GEOD-57667 | biostudies-arrayexpress

siPools: highly complex but accurately defined siRNA pools eliminate Off-target effects (HuGene-2_0)

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. dsRNA fragments of more than 30bp length may trigger interferon response in mammalian cells, depending on the cell type as well as length and concentration of the dsRNA. To demonstrate that complex siRNA pools (siPools) do not contain trace amounts of such longer dsRNA species and therefore do not trigger interferon response, MCF7 cells which exhibit sensitive interferon response, were transfected with a siPool targeting human SCYL1, consisting of 60 siRNA at a total siRNA concentration of 3nM. As positive control, MCF7 cells were transfected with an RNAseIII generated mixture of dsRNAs (esiRNAs) at equal concentration (weight/volume). Mock transfected cells served as negative control. Every sample was tested in biological triplicates. Total RNA was extract 48h after transfection for affimetrix expression analysis.

2014-05-15 | E-GEOD-57646 | biostudies-arrayexpress

Project description:siPools: highly complex but accurately defined siRNA pools eliminate Off-target effects

| PRJNA247539 | ENA

Homo sapiens

Project description:siPools: highly complex but accurately defined siRNA pools eliminate Off-target effects (HuGene-2_0)

| PRJNA247557 | ENA

Homo sapiens

Project description:siPools: highly complex but accurately defined siRNA pools eliminate Off-target effects (HuGene-1_0 ENST)

| PRJNA247505 | ENA

microRNA-like off-target transcript regulation by siRNAs

2009-02-01 | GSE14073 | GEO

The effects of knockdown of PML by different individual siRNAs in HUVEC cells

Project description:To study the potential target genes regulated by PML in endothelial cells, we carried out siRNA-mediated knockdown of PML in HUVEC cells. To eliminate the off-target effects of siRNAs, we utilized two different siRNAs. Only the genes changed in the same pattern following both siRNAs transfection are considered as potential PML-knockdown responsive genes.

2012-05-31 | GSE29238 | GEO

microRNA-like off-target transcript regulation by siRNAs

Project description:siRNAs mediate sequence-specific gene silencing in cultured mammalian cells but also silence unintended transcripts. Many siRNA off-target transcripts match the guide-strand ‘‘seed region,’’ similar to the way microRNAs match their target sites. The extent to which this seed-matched, microRNA-like, off-target silencing affects the specificity of therapeutic siRNAs in vivo is currently unknown. Here, we compare microRNA-like off-target regulations in mouse liver in vivo with those seen in cell culture for a series of therapeutic candidate siRNAs targeting Apolipoprotein B (APOB). Each siRNA triggered regulation of consistent microRNA-like off-target transcripts in mouse livers and in cultured mouse liver tumor cells. In contrast, there was only random overlap between microRNA-like off-target transcripts from cultured human and mouse liver tumor cells. Therefore, siRNA therapeutics may trigger microRNA-like silencing of many unintended targets in vivo, and the potential toxicities caused by these off-target gene regulations cannot be accurately assessed in rodent models. Hepa1-6 mouse hepatoma cell line and HUH7 and PLC/PRF/5 human hepatoma cell lines were transfected in 6-well plates using Lipofectamine RNAiMAX and siRNA duplexes at a final concentration of 10 nM. For in vitro analysis, RNA was extracted at 6, 12, 24, and 48 h post-transfection. For in vivo studies, mouse livers were harvested 3 d following a single administration of APOB siRNA (3 mg/kg) formulated in lipid nanoparticles. For details, please see: J. Burchard, A.L. Jackson, V. Malkov, R.H.V. Needham, Y. Tan, S.R. Bartz, H. Dai, A.B. Sachs and P.S. Linsley. microRNA-like off-target transcript regulation by siRNAs is species specific. RNA 15 (2009)

2009-01-31 | E-GEOD-14073 | biostudies-arrayexpress

Synthesis of 2'-formamidonucleoside phosphoramidites for suppressing the seed-based off-target effects of siRNAs [RNA-seq]

Project description:To investigate effects of siRNA with 2'-formamidonucleoside phosphoramidites (2'-FA) modifications on genome-wide off-target, we analyzed gene expression profile of HeLa cells transfected by their siRNAs.

2024-09-30 | GSE274426 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data