Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA247505 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:siPools: highly complex but accurately defined siRNA pools eliminate Off-target effects (HuGene-2_0)
| PRJNA247557 | ENA
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.
2014-05-15 | GSE57667 | GEO
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.
2014-05-15 | GSE57646 | GEO
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
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:This SuperSeries is composed of the following subset Series: GSE26018: Crosstalk between gene body DNA methylation, H3K9me3 and H3K36me3 chromatin marks and transcription [HuEx-1_0-st] GSE26019: Crosstalk between gene body DNA methylation, H3K9me3 and H3K36me3 chromatin marks and transcription [HuGene-1_0-st] GSE26038: Crosstalk between gene body DNA methylation, H3K9me3 and H3K36me3 chromatin marks and transcription [HuEx-1_0-st, transcript] GSE26040: Relationship between gene body DNA methylation and intragenic H3K9me3 and H3K36me3 chromatin marks Refer to individual Series
2011-03-31 | E-GEOD-26020 | biostudies-arrayexpress
Project description:Chronic infection of M. hyorhinis is postulated to be associated with cancer cell migration and invasion. To explore the mechanisms of M. hyorhinis-promoted invasiveness, we performed Affymetrix genechip (HuGene-1_0-st) analysis to examine differential gene expression profiles between non-infected and infected gastric cancer cells. We used microarrays to detail global programme of gene expression and identified distinct classes of upregulated genes after M. hyorhinis infection of gastric cancer cell lines.
2013-11-22 | GSE52638 | GEO
Project description:Human synovial biopsies were collected from normal and osteoarthritic joints. CD90 positive cells were isolated and confirmed to have multipotent differentiation capacity. An n=2 of normal and n=2 OA lines were run on the HuGene-1_0-st-v1 array.
2022-02-18 | E-MTAB-11492 | biostudies-arrayexpress
Project description:H3R17 methylation inhibitor TBBD associated differential gene expression in embryoid bodies was assessed by microarray analysis treated with 10uM TBBD for 48 hours compared to DMSO control treated Ebs Affymetrix one-color experiment,Organism: Homo sapiens[HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array
2015-07-01 | E-GEOD-64001 | biostudies-arrayexpress