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Gapdh sirna

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GAPDH siRNA is a small interfering RNA (siRNA) designed to target and silence the expression of the GAPDH (Glyceraldehyde 3-phosphate dehydrogenase) gene. GAPDH is a commonly used housekeeping gene involved in glycolysis. The GAPDH siRNA can be used to investigate the role of GAPDH in cellular processes.

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12 protocols using gapdh sirna

1

Galectin-3 Silencing in HPMECs

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The siRNAs were purchased from GenePharma Corporation (Shanghai, China). The sequences are as follows: siNC: 5′-UUCUCCGAACGUGUCACGUTT-3′; GAPDH siRNA:5′-UGACCUCAACUACAUGGUUTT-3′; galectin-3 siRNA:5′-GCUCACUUGUUGCAGUACATT-3′; HPMECs were seeded into 10 cm culture dishes and incubated for 24 h. Then, the 70–80% confluent HPMECs were transfected with negative control group—siNC, positive control group—GAPDH siRNA and target galectin-3 siRNA using Lipofectamine 3000 (Thermo Fisher, USA) according to the manufacturer’s instructions. The final concentration of the siRNA solution was 50 nM.
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2

Optimizing siRNA Complexation with Peptide Carriers

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GAPDH siRNA (Thermo Scientific, Loughborough, UK; sequences used were sense 5′ UGG UUU ACA UGU UCC AAU AUU 3′, antisense 5′ Phosphate U AUU GGA ACA UGU AAA ACC UU 3′) was mixed in RNAse-free water with varying concentrations of either SMoC, PySSCH2CH2CO-RRRR-NH2, 9 (R4SSPy) or PySSCH2CH2CO-RRRRRRRR-NH2, 10, (R8SSPy), (Peptide Synthetics, Ltd, UK) in the molar ratios of 1/1, 1/5, 1/10, 1/20 and 1/50. The final siRNA concentration was 17 μm in 100 μL of water (1.7 nmol) in each case. The complexes were incubated for 30 min at room temperature. The samples were diluted with 2× RNA loading dye (Fermentas, now Thermo Scientific) containing ethidium bromide (composition 95% formamide, 0.025% SDS, 0.025% bromophenol blue, 0.025% xylene cyanol FF, 0.025% ethidium bromide, 0.5 mm EDTA) and analyzed by gel electrophoresis on a 1% agarose gel prepared using 10× MOPS buffer [0.4 m MOPS (pH 7), 0.1 m sodium acetate, 0.01 m EDTA (pH 8)], loading 25 μL of sample into each well. The gel was run at 5V/cm till the blue dye had migrated 2/3 of the gel. The gels were analyzed by UV illumination and the ethidium bromide bands quantified using the ImageJ software (NIH, Bethesda, MD, USA). The EtBr intensities were plotted, a dose–response curve fitted and EC50 values calculated using the Origin software (OriginLab, Northampton, MD, USA).
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3

Lipid-Based Nanoparticle Drug Delivery Protocol

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Cholesterol was purchased from Sigma Aldrich, while distearoyl-sn-glycerol-3-phosphocholine (DSPC) and PEG2000-DMG were obtained from Avanti Polar Lipids. Dual HeLa and Caco-2 cells were purchased from American Type Culture Collection (Manassas, VA). Porcine pepsin, pancreatin, bile salts, and mucin type II were obtained from Sigma (St Louis, MO). Dulbecco’s Modified Eagles Media (DMEM), trypsin, penicillin/streptomyocin, phosphate buffered saline (PBS), fetal bovine serum (FBS), and GAPDH siRNA were purchased from Thermo Fisher (Waltham, MA). Corning BioCoat HTS 1 µm porous support Transwell plates, basal seeding medium (BSM), Corning EnteroSTIM enterocyte differentiation medium (EDM), and MITO + serum extender were obtained from VWR (Radnor, PA). Anti-firefly luciferase siRNA (siLuc) was purchased from Dharmacon (Lafayette, CO).
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4

Gene Silencing Using siRNA Knockdown

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Atg5, Wnt5a and MMP-3 siRNAs for gene silencing were acquired commercially (sc-41446, sc-41113 and sc-37265, respectively; Santa Cruz Biotechnology Inc.) and were transfected into cultured cells using an siRNA reagent system (Santa Cruz Biotechnology Inc.) according to the manufacturer’s protocol. GAPDH siRNA and control siRNA (Thermo Scientific, Lafayette, CO, USA) with no known homogeny for any vertebrate sequence were used as positive and negative controls, respectively.
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5

Transient siRNA knockdown of B7-H3

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Cells were transfected at 50% confluency for transient siRNA transfection using a control siRNA (4390843) (Thermofisher, Australia), GAPDH siRNA (4390849) and two different silencer select siRNAs targeting B7-H3 (s37290 and s37288) (Thermofisher, Australia) at 10 nM final concentration with Lipofectamine RNAiMAX (Invitrogen, Australia) according to manufacturer's protocol. Cells were incubated with siRNA complex for 72 hours and then collected for further experiments.
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6

TFEB Knockdown in Cell Cultures

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Cells were transiently transfected with TFEB siRNA (100 nmol/L; Ambion, USA), by using Lipofectamine® RNAiMAX Transfection reagent (Gibco, USA). The protocol was synthesized according to the manufacturer’s protocol. GAPDH siRNA was used as a control (40 nmol/L; Ambion, USA). Transfection efficiency was >70% assessed by BLOCK-iT™ Alexa Fluor® Red Fluorescent Control (Ambion, USA) and western blotting. Cells were transfected with siRNA for 24 h before experiments.
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7

Ceacam-1 siRNA Transfection in PBMCs

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Seven frozen PBMC samples were electroporated with a Neon transfection kit and device (Invitrogen). Cells (3 × 105) were incubated for 18 h with 10 ng/ml of IL-2 (Peprotech) and 10 ng/ml of IL-15 (Peprotech) and resuspended in 10 µl of buffer T (Neon kit, Invitrogen). Ceacam-1 siRNA (Entrez Gene ID 634; detected transcripts NM_001024912.2, NM_001205344.1, and NM_001712.4) or negative control siRNA (at a final concentration of 100 nM; Ambion) were added to the cell suspension. Ten microliters of the suspension were electroporated (1,700 V, 20 ms, three pulses). GAPDH siRNA (Ambion) was used as a positive control to evaluate efficiency of the silencing. Cells were incubated for 24 h at 37°C and 5% CO2 and then stimulated in anti-CD16-coated plate (1 µg/ml) for 5 h at 37°C and 5% CO2 in the presence of CD107a antibody. Brefeldin A (eBioscience) and Monensin (eBioscience) were added during the last 4 h of incubation. Surface markers and functions by intracellular staining were assessed by flow cytometry as described earlier.
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8

Silencing NEU1 in THP-1 Macrophages

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Silencer™ predesigned siRNA (ID:8481, Ambion) targeting exon 2 of the human NEU1 gene were used to silent NEU1 [7 (link), 26 (link)]. THP-1 cells (1.5 million) were transfected in 6-well culture dishes with either 50 nM NEU1 siRNA or negative control siRNA (Ambion) using INTERFERin reagent (Polyplus Transfection) according to the protocol provided by the manufacturer. Twenty-four hours after transfection, THP-1 cells were counted, transferred in 12-well culture dishes (500,000/well) and differentiated into adherent macrophages using 50 nM PMA for 72 h before measurement of sialidase activity. GAPDH siRNA (Ambion) was used as a positive control for optimization of transfection conditions and siRNA efficacy was verified at the protein level by Western blotting.
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9

Investigating TRPM2, NLRP3, and Oxidative Stress

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Cells were transiently transfected with TRPM2 specific small interfering RNA (siRNA) (60 nmol/L; Ambion, US), NLRP3 siRNA (100 nmol/L; Santa Cruz Biotechnology, US), ASC siRNA (100 nmol/L; Ambion, US), caspase-1 siRNA (100 nmol/L; Ambion, US) or p47 phox siRNA (80 nmol/L; Ambion, US) by using Lipofectamine® RNAiMAX Transfection reagent (Gibco, US). The protocol was synthesized according to the manufacturer’s protocol. GAPDH siRNA was used as a control (40 nmol/L; Ambion, US). Transfection efficiency was > 70% assessed by BLOCK-iT™ Alexa Fluor® Red Fluorescent Control (Ambion, US) and western blotting. Cells were transfected with siRNA for 24 h before experiments.
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10

Characterization of Engineered Amphiphysin2 and N-WASP Constructs

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GFP-tagged human amph2-K573X, amph2-K575X, amph2-D151N, and amph2-R154Q were described in (Nicot et al, 2007 (link)). GFP-tagged N-WASP-FL or VCA (Lommel et al, 2001 (link)) were a gift from Theresia Stradal. pTdT-VCA has been generated by NheI-BsrGI replacement of GFP with pTdT in GFP-VCA. pcDNA GFP was a gift from Alexis Gautreau. RFP-KASHΔL and RFP-SR-KASH were previously described in (Luxton et al, 2010 (link)). The following siRNAs were purchased from Life Technologies; amph2 exon3 siRNA (GGAUCUUCGGACCUAUCUGtt); N-WASP siRNAs (#1: GGCUAAUCCACUCUGAGUAtt and #2: GGCUAUUUUUUAGCAAAGAtt); GAPDH siRNA (cat # AM4624); DNM2 siRNA (GCGAAUUGAAGGCUCGGGAtt), MTM1 siRNA (CGCAUAUCAAACUCAGAAtt), amph2 exon11 siRNA (CGGCUGCGCAGAAAGAAGAtt), Kif5b siRNA (TAGACCGGATAAAGGAAGCAG), and Map7 siRNA (CAGAUUAGAUGUCACCAAUTT).
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