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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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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. mRNA profiles of HCT 116 cells after the transfection of siRNAs or blank control by deep sequencing, using HiSeq 2000

ORGANISM(S): Homo sapiens

SUBMITTER: Zhenzhen Liu

PROVIDER: E-GEOD-62968 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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

Li Chunyan C Liu Zhenzhen Z Yang Fang F Liu Wensheng W Wang Di D Dong Encheng E Wang Yu Y Wu Chung-I CI Lu Xuemei X

Oncotarget 20150801 25

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-ta ...[more]

PMID: 26057633

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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.

2015-07-01 | GSE62968 | GEO

Gene silencing of BSK65-MONO1 (RNF185) and of its natural antisense RNA (RNF185-AS) using siRNAs

Project description:Microarray profiles of native HeLa cells and RNF185/BSK65 gene silenced HeLa cells using siRNAs LMG2 and LMG4 were monitored using Affymetrix U133 Plus 2.0 microarrays. Two independent microarray assays of each analysis were used for the comparison of native vs. siRNA treated HeLa cells with LMG2 and LMG4.

2013-06-07 | E-GEOD-47685 | biostudies-arrayexpress

Phenocopy

Project description:Comprehensive in vitro expression profiling of small chemical compound inhibitors of TGFbR1 kinase activity. Additional file E-MTAB-265.additonal.1.zip contains excel file with Taqman data validating the array normalization method

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smalRNA seq of IPSC-cardiomyocytes treated with exosomes before hypoxic stiumli

Project description:This experiment aimed to investigate whether exosomess released by IPSC-cardiomyocytes during hypoxia can positively influence cardiac electrophysiology and miRNA expression during hypoxic stress. A multielectrode array (MEA) system was used as an in vitro method of recording real-time cardiac electrophysiological activity, highlighting the biological effects facilitated by exosomes. Additionally, miRNA-sequencing was performed to compare miRNA expressions in exosome-preconditioned and non-preconditioned IPSC-cardiomyocytes, elucidating important modulators of cardiac electrophysiology.

2024-04-01 | E-MTAB-13912 | biostudies-arrayexpress

The effect of CuO nanoparticles on gene expression patterns in Daphnia magna

Project description:There is still a lot of contradiction on whether metal ions are solely responsible for the observed the toxicity of ZnO and CuO nanoparticles to aquatic species. While most tests have studied nanoparticle effects at organismal levels (e.g. mortality, reproduction), effects at suborganismal levels may clarify the role of metal ions, nanoparticles and nanoparticle aggregates. In this study, the effect of ZnO, CuO nanoparticles and zinc, copper salts was tested on the gene expression levels in Daphnia magna. D. magna was exposed during 96 hours to 10% immobilization concentrations of all chemicals, after which daphnids were sampled for a differential gene expression analysis using microarray. When comparing the nanoparticle exposed daphnids (ZnO or CuO) to the metal salt exposed daphnids (zinc or copper salt), the microarray results showed no significantly differentially expressed genes. These results indicate that the toxicity of the tested ZnO and CuO nanoparticles to D. magna caused is solely caused by toxic metal ions. 4 replicate exposures of ZnO nanoparticles, ZnCl2, Blank (for Zn); 4 replicate exposures of CuO nanoparticles, CuCl2.2H2O, Blank (for Cu); Individual reference design with swapped dyes for zinc (e.g. ZnO-REFZn; REFZn-bl) and copper exposure (e.g. CuO-REFCu; REFCu-bl); Zinc reference sample is a mixture of equal aliquots of ZnO nanoparticle, ZnCl2 and blank; Copper reference sample is a mixture of equal aliquots of CuO nanoparticle, CuCl2.2H2O and blank

2014-03-01 | E-GEOD-54738 | biostudies-arrayexpress

The effect of ZnO nanoparticles on gene expression patterns in Daphnia magna

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Enhanced engraftment, proliferation, and therapeutic potential in heart using optimized iPSC-derived cardiomyocytes

Project description:Human pluripotent stem cell-derived cardiomyocytes (CMs) are a promising tool for cardiac cell therapy. To optimize graft cells for cardiac reconstruction, we compared the engraftment efficiency of intramyocardially-injected undifferentiated-induced pluripotent stem cells (iPSCs), day4 mesodermal cells, and day8, day20, and day30 purified iPSC-CMs after initial differentiation by tracing the engraftment ratio (ER) using in vivo bioluminescence imaging. This analysis revealed the ER of day20 CMs was significantly higher compared to other cells. Transplantation of day20 CMs into the infarcted hearts of immunodeficient mice showed significant functional improvement. Moreover, the imaging signal and ratio of Ki67-positive CMs at 3 months post injection indicated engrafted CMs proliferated in the host heart. Although this graft growth reached a plateau at 3 months, histological analysis confirmed progressive maturation from 3 to 6 months. These results suggested that day20 CMs had very high engraftment, proliferation, and therapeutic potential in host mouse hearts. Differentiated cells, N=10 Undifferentiated pluripotent stem cells, N=1 Heart samples, N=6

2016-07-03 | E-GEOD-60634 | biostudies-arrayexpress

Gene expression profile of Huh7 cells upon knock-down of FOXA2 or FOXA2-DS-S

Project description:We used siRNAs to knock-down the gene FOXA2 and the positionally-conserved ncRNA (pcRNA) FOXA2-DS-S is Huh7. We have shown that FOXA2 regulates its own expression by binding its promoter, but it can also affect the expression of the associated pcRNA FOXA2-DS-S. At the same time, we have shown that FOXA2-DS-S is necessary for the expression of the FOXA2 gene. These data suggest that the pcRNA acts locally, in cis, to regulate the expression of FOXA2. With this microarray experiment with aimed to explore further the genome-wide transcriptional effects of FOXA2-DS-S or FOXA2 knock-down.

2018-01-09 | E-MTAB-4517 | biostudies-arrayexpress

Affymetrix array of three pancreatic cancer cells treated with tumour treating fields upon combination with mild hyperthermia

Project description:Tumor Treating Fields (TTFields) disturbs mitosis and consequently leads to cell cycle arrest and cell death. Mild hyperthermia induces cancer cell death by apoptosis,leading to DNA damage and disturbing DNA repair. Thus, when mild hyperthermia is combined with TTFields, the anti-tumor effect could be augmented. This prompted the hypothesis for the present thesis: TTFields and mild hyperthermia as synergistic modalities in Pancreatic ductal adenocarcinoma (PDAC) treatment could probably enhance antitumor efficacy and abate individual toxic effects through distinct and overlapping mechanisms target the tumor cell. Our established PDAC cell line (Bx-GEM) was treated with TTFields and TTFields with mild hyperthermia and was examined by microarray. 500 ng mRNA was checked for quality control and the concentration was measured again. Subsequently, gene expression profiling was performed using human HuGene-2_0-st-type array from Affymetrix.

2021-03-17 | E-MTAB-10270 | biostudies-arrayexpress

Genome-wide prediction of genes targeted by titrated levels of miR-17~92

Project description:The miR-17-92 cluster targets mRNAs involved in distinct pathways which either promote or inhibit tumor progression. However, the cellular and molecular mechanisms underlying miR-17~92 cluster mediated pro- or anti- tumorigenic effects has not been studied. In this study, we found that inhibition of colon cancer progression is dictated by quantitatively controlling expression of the miR-17~92 cluster. To identify molecular mechanisms giving rise to the different growth/metastasis patterns, we profiled gene expression in miR-Ctrl, miR-17~92Med and miR-17~92Hi cells using Affymetrix Murine GeneST Arrays. Total RNA from miR-Ctrl, miR-17~92Med and miR-17~92Hi cells (3 subclones of each group) was isolated and subsequently processed for microarray hybridization using Affymetrix.

2014-06-01 | E-GEOD-55631 | biostudies-arrayexpress

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