Sirna duplexes

Manufactured by Thermo Fisher Scientific

Sourced in United States

SiRNA duplexes are synthetic, double-stranded RNA molecules that are designed to target and silence specific genes within cells. They function by binding to and degrading the target mRNA, thereby reducing the expression of the corresponding protein.

Automatically generated - may contain errors

Lab products found in correlation

Lipofectamine 2000, by Thermo Fisher Scientific (18 mentions) Lipofectamine rnaimax, by Thermo Fisher Scientific (12 mentions) Negative universal control, by Thermo Fisher Scientific (7 mentions) Lipofectamine rnaimax reagent, by Thermo Fisher Scientific (5 mentions) Sirna oligonucleotide duplexes, by Merck Group (4 mentions) Lipofectamine imax, by Thermo Fisher Scientific (3 mentions) Lipofectamine 3000, by Thermo Fisher Scientific (2 mentions) Jetprime, by Polyplus Transfection (2 mentions) Rnaimax transfection reagent, by Thermo Fisher Scientific (2 mentions) Sirna duplexes, by RiboBio (2 mentions) Ambiv neg ctl cat 4457287, by Thermo Fisher Scientific (2 mentions) Gapdh sirna cat, by Thermo Fisher Scientific (2 mentions) Sirna duplexes, by GenePharma (2 mentions) Monoclonal anti flag m2 antibody f1804, by Merck Group (1 mentions) Dithiothreitol (dtt), by Merck Group (1 mentions) Nigericin, by Merck Group (1 mentions) N ethylmaleimide, by Merck Group (1 mentions) Ultrapure lps, by InvivoGen (1 mentions) Complete protease inhibitor cocktail, by Roche (1 mentions) Terbium 3 chloride, by Merck Group (1 mentions)

Spelling variants of this product

SiRNAs (258 citations) SiRNA duplex (16 citations) Stealth RNAi siRNA Duplex Oligoribonucleotides (6 citations) SiRNA duplex oligonucleotides (6 citations) Stealth siRNA duplex (5 citations) SiRNA duplex oligoribonucleotides (4 citations) Stealth RNAi siRNA duplex (3 citations) Control nonspecific siRNA duplex (3 citations) Stealth RNAi siRNA GFP Reporter Control duplex (2 citations) HPLC purified duplex siRNA for human and mouse genes (2 citations)

65 protocols using sirna duplexes

Reverse Transfection of HUVECs with siRNA

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HUVECs were reverse transfected in 6‐ or 96‐well plates with siRNA duplexes as follows.
20 nm non‐targeting control siRNA:
5′‐UAAGGCUAUGAAGAGAUAC‐3′
5′‐AUGUAUUGGCCUGUAUUAG‐3′
5′‐AUGAACGUGAAUUGCUCAA‐3′
5′‐UGGUUUACAUGUCGACUAA‐3′
20 nm USP8 siRNA:
5′‐UGAAAUACGYGACUGUUUA‐3′
5′‐GGACAGGACAGUAUAGAUA‐3′
5′‐AAAUAAAGCUCAACGAGAA‐3′
5′‐GGCAAGCCAUUUAAGAUUA‐3′
All siRNA duplexes were from ThermoFisher and used according to the manufacturer's instructions. Endothelial cells were incubated for 6 h with siRNA duplexes using a previously described lipid‐based transfection protocol 30. After 72 h, cells were processed for lysis and immunoblotting as previously described.

Smith G.A., Fearnley G.W., Abdul‐Zani I., Wheatcroft S.B., Tomlinson D.C., Harrison M.A, & Ponnambalam S. (2015). VEGFR2 Trafficking, Signaling and Proteolysis is Regulated by the Ubiquitin Isopeptidase USP8. Traffic (Copenhagen, Denmark), 17(1), 53-65.

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siRNA-mediated CHOP knockdown

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The siRNA duplexes used in this study were purchased from Invitrogen (Carlsbad, CA, USA) and have the following sequences: CHOP (5’-GAGCUCUGAUUGACCGAAUGGUGAA-3′). Negative Universal Control (Invitrogen, CA, USA) was used as the control. Cells were seeded on 6-well plates and cultured for 24 h in complete growth medium, and then were transfected with siRNA duplexes against human CHOP (100 nM) or control siRNA by lipofectamine 3000 (Invitrogen, CA, USA) according to manufacturer’s instructions.

Chen W., Li P., Liu Y., Yang Y., Ye X., Zhang F, & Huang H. (2018). Isoalantolactone induces apoptosis through ROS-mediated ER stress and inhibition of STAT3 in prostate cancer cells. Journal of Experimental & Clinical Cancer Research : CR, 37, 309.

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Modulating AMPK and CaMKKβ Signaling

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Cells were transfected in 1 ml OPTIMEN containing 4 μg lipofectamine iMax (Invitrogen, Carlsbad, CA), with 100 nM AMPK specific small interfering RNA (siRNA) duplexes (5'-CCCAUAUUAUUUGCGUGUAdTdT-3' and 5'-UACACGCCAAAUAAUAUGGGdTdT-3') (Ambion-Life Technologies, Carlsbad, CA, USA), 100 nM CaMKKβ selective si RNA (5'-GCUCCUAUGGUGUCGUCAAdTdT-3' and 5'-UUGACGACACCAUAGGAGCdTdT-3') or control scrambled RNA according to manufacturer’s protocols (Invitrogen, Carlsbad, CA). At 48 h after transfection, the medium was removed and replaced for DMEM. At dedicated time points after transfection, cells were used for MTT cell viability assays or Western blot.

Bort A., Sánchez B.G., Spínola E., Mateos-Gómez P.A., Rodríguez-Henche N, & Díaz-Laviada I. (2019). The red pepper’s spicy ingredient capsaicin activates AMPK in HepG2 cells through CaMKKβ. PLoS ONE, 14(1), e0211420.

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Transient AMPK Silencing Assay

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Cells were transfected in 1 mL OPTIMEM containing 4 μg Lipofectamine iMax (Invitrogen) with 100 nm AMPK‐specific small interfering RNA (siRNA) duplexes (Ambion‐Life Technologies, Carlsbad, CA, USA) or scrambled RNA (control) according to the manufacturer's protocols (Invitrogen). At 48 h after transfection, the medium was removed and replaced with DMEM. At the indicated time points after transfection, cells were used for MTT cell viability assays or western blot analysis.

Bort A., Sánchez B.G., Mateos‐Gómez P.A., Vara‐Ciruelos D., Rodríguez‐Henche N, & Díaz‐Laviada I. (2019). Targeting AMP‐activated kinase impacts hepatocellular cancer stem cells induced by long‐term treatment with sorafenib. Molecular Oncology, 13(5), 1311-1331.

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GSDMD Protein Detection Protocol

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Polyclonal anti-human GSDMD was from Novus Biologicals (NBP2-33422) or Proteintech (20770-1-AP). Monoclonal anti-haemagglutinin (F-7) antibody (sc-7392) was from Santa Cruz Biotechnology. Monoclonal anti-Flag M2 antibody (F1804), monoclonal anti-human α-tubulin antibody (T5168) and monoclonal anti-mouse caspase-11 antibody (C1354) were from Sigma-Aldrich. Polyclonal anti-human Na⁺/K⁺-ATPase α1 (ATP1A1) antibody (#3010) was from Cell Signaling. c-MYC (9E10) monoclonal antibody (MMS-15P) was from Covance. Monoclonal anti-human perforin antibody (3465-6-250) and polyclonal anti-human granulysin antibody (AF3138) were from Mabtech and Novus, respectively. N-ethylmaleimide, 2ME, DTT, terbium(III) chloride, DPA (dipicolinic acid) and nigericin were from Sigma-Aldrich. Ultrapure LPS and Pam3CSK4 were from InvivoGen. The complete protease inhibitor cocktail was from Roche. siRNA duplexes targeting Gsdmd (s87492; 5′-GGUGAACAUCGGAAAGAUUTT-3′) and the nonspecific control siRNA (CTL, 4390843) were from Ambion.

Liu X., Zhang Z., Ruan J., Pan Y., Magupalli V.G., Wu H, & Lieberman J. (2016). Inflammasome - activated gasdermin D causes pyroptosis by forming membrane pores. Nature, 535(7610), 153-158.

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p62/SQSTM1 Knockdown and Autophagy Regulation

Cited 1 time

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A set of p62/SQSTM11 shRNA vectors (SHCLNG-NM_003900), and a non-target shRNA control vector were purchased from Sigma-Aldrich (St. Louis, MO) for the p62/SQSTM1 knockdown experiments. Lentivirus production and viral infection were done as previously described [23] (link). Small interfering RNA (siRNA) duplexes were purchased from Ambion (Austin, TX) targeting ATG7 (ID# s20650 and s20651). Negative Control #1 siRNA was used as control. siRNAs (30 µM per 100 µl transfection solution) were electroporated using Lonza's Nucleofector and the Cell Line Neucleofection kit V (Walkersville, MD) As described in [23] (link)

Kuo W.L., Sharifi M.N., Lingen M.W., Ahmed O., Liu J., Nagilla M., Macleod K.F, & Cohen E.E. (2014). p62/SQSTM1 Accumulation in Squamous Cell Carcinoma of Head and Neck Predicts Sensitivity to Phosphatidylinositol 3-Kinase Pathway Inhibitors. PLoS ONE, 9(3), e90171.

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siRNA Transfection Protocol for Co-Depletion Experiments

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All siRNA duplexes used in this study were purchased from Ambion and are listed in Table S2. siRNA oligos were transfected at a final concentration of 10 nM using Lipofectamine RNAiMax (Invitrogen) as indicated. For co-depletion experiments, the respective siRNAs were transfected at a final concentration of 10 nM + 10 nM of each oligonucleotide and the total amount of oligonucleotides was kept equal by transfecting a non-targeting siRNA (CTNL) in the single depletion samples.

Bolck H.A., Przetocka S., Meier R., von Aesch C., Zurfluh C., Hänggi K., Spegg V., Altmeyer M., Stebler M., Nørrelykke S.F., Horvath P., Sartori A.A, & Porro A. (2022). RNAi Screening Uncovers a Synthetic Sick Interaction between CtIP and the BARD1 Tumor Suppressor. Cells, 11(4), 643.

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SIRT1 Knockdown Assay in Cells

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Cells were seeded into 60 mm culture dishes at 18–24 h prior to transfection. siRNA transfection experiments were performed using SuperFect (Qiagen, Valencia, CA, USA) essentially following the manufacturer’s instructions. Transfection-ready control siRNA duplexes were purchased from Ambion (Austin, TX, USA), and SIRT1-targeting siRNA designed against nucleotides (5′-TGA AGT GCC TCA GAT ATT A-3′ and 5′-TAA TAT CTG AGG CAC TTC A-3′) of the mouse SIRT1 mRNA sequence were synthesized by Bioneer (Daejeon, Korea). Following incubation for 6 h, cells were provided with fresh medium and grown for an additional 38 h, at which point they were treated with the reagents for the indicated period of time. The effects of gene silencing were verified by Western blot analysis.

Hwang J.S., Choi H.S., Ham S.A., Yoo T., Lee W.J., Paek K.S, & Seo H.G. (2015). Deacetylation-mediated interaction of SIRT1-HMGB1 improves survival in a mouse model of endotoxemia. Scientific Reports, 5, 15971.

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AMPK Silencing Impacts Cell Viability

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Cells were transfected in 1 mL OPTIMEM containing 4 μg Lipofectamine iMax (Invitrogen) with 100 nM AMPK-specific small interfering RNA (siRNA) duplexes (5′-CCCAUAUUAUUUGCGUGUAdTdT-3′ and 5′-UACACGCCAAAUAAUAUGGGdTdT-3′) (Ambion-Life Technologies, Carlsbad, CA, USA) or scrambled RNA (control) according to the manufacturer’s protocols (Invitrogen). At 48 h after transfection, the medium was removed and replaced with RPMI. At the indicated time points after transfection, cells were used for MTT cell viability assays or Western blot analysis.

Sánchez B.G., Bort A., Vara-Ciruelos D, & Díaz-Laviada I. (2020). Androgen Deprivation Induces Reprogramming of Prostate Cancer Cells to Stem-Like Cells. Cells, 9(6), 1441.

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Silencing Exosome and Stress Pathway Genes

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The siRNA duplexes targeting EXOSC3 (s27230, s27231), EXOSC4 (s29112, s29113), EXOSC9 (s10736, s10734), EXOSC10 (s10737, s10738), BIK (s1989), and SESN2 (s38098) were purchased from Ambion. Cells were transfected with RNA duplexes using Lipofectamine RNAiMAX (Thermo Fisher Scientific). Silencer Select negative control siRNA #2 (Ambion) was used as a control.

Taniue K., Tanu T., Shimoura Y., Mitsutomi S., Han H., Kakisaka R., Ono Y., Tamamura N., Takahashi K., Wada Y., Mizukami Y, & Akimitsu N. (2022). RNA Exosome Component EXOSC4 Amplified in Multiple Cancer Types Is Required for the Cancer Cell Survival. International Journal of Molecular Sciences, 23(1), 496.

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