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17 protocols using accell sirna delivery medium

1

Keap1 and Nrf2 siRNA Knockdown

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Cells were transiently treated with Keap1 siRNA and/or Nrf2 siRNA using Accell siRNA delivery medium (Dharmacon, USA) according to the manufacturer’s instructions. Cells (2 × 105/well) were added to wells of 12-well plates and cultivated overnight at 37 °C in an atmosphere of 5% CO2. Then, 2 µm of Keap1 and Nrf2 siRNA (Smartpool, Dharmacon) in 1× siRNA buffer (Dharmacon) were transferred to each well, cultivated for 72 h at 37 °C and 5% CO2, and lysed. Keap1 and/or Nrf2 silencing efficiency was examined by qPCR.
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2

Antagomir-Mediated Silencing of miRNAs

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Antagomirs are chemically engineered single strand RNA oligonucleotides that silence specific miRNA in vitro in cultured cells and in vivo in animals efficiently [39 (link), 40 (link)]. As previously described [39 (link)], antagomirs against specific DLK1-Dio3 miRNAs were designed based on mature murine miRNA sequence from miRBase (http://www.mirbase.org/), and then synthesized by GE Dharmacon (Lafayette, CO, USA). The sequences of scrambled control specific DLK1-Dio3 miRNAs were listed in S1 Table.
As previously reported [40 (link)], to inhibit function of a specific miRNA in splenocytes, freshly isolated splenocytes were washed with PBS with 0.5% BSA, resuspended in serum free Accell siRNA delivery medium (GE Dharmacon) supplemented with 1μM specific antagomir or scrambled control antagomir at 10x106/ml, and then incubated in the cell incubator (37°C, 5% CO2) for 1.5–2 hrs. After incubation, the treated cells were pelleted and resuspended with complete RPMI medium supplemented with 0.1μM respective antagomirs at 5x106/ml and plated into 24 well plate for culture. Twenty-four hours after antagomirs treatment, the cells were stimulated with lipopolysaccharide (LPS, 500ng/ml, from Sigma-Aldrich) for the designated time. The supernatant were collected for analysis of cytokine production.
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3

MUC15 Silencing in Differentiated hNECs

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Differentiated hNECs were transfected with 2 μM non-targeting siRNA (NT-siRNA) or MUC15 siRNA in Accell siRNA delivery medium (GE Healthcare Dharmacon, Inc.) for 3 times at − 48, − 24 and 6 hpi. hNECs were then harvested at 24 and 48 hpi for RT-qPCR analysis.
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4

Nucleofection and siRNA Silencing in OT1 T Cells

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10 mil of OT1 cells were nucleofected with 1 μg of each vector using the Mouse T-cell Nucleofector Kit (VPA-1006, Lonza) and Amaxa nucleofector device (program X-01, unstimulated T cells). The nucleofected T cells were rested for 6 hours in a mouse T cell nucleofector medium (VZB-1001, Lonza), and stimulated with CD3/CD28 beads for 24 hours before proceeding with a luciferase assay. For siRNA silencing, 1 mil of OT1 cells was resuspended in 750 ul of Accell siRNA delivery medium (Dharmacon, B-005000) containing 7.5ul of each siRNA resuspended in 1x siRNA buffer (Dharmacon, B-002000-UB-100). After 48hrs, the cells were activated and assayed for WB, activation, and proliferation. The following siRNA SMARTpool (Dharmacon) products were used: Notch1: E-041110, Il2rb: E-042082, Psat1: E-056759, Eef1a1: E-042142, Eef2: E-042517, Ipo5: E-042367, non-targeting control: D-001810.
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5

Splenic DCs siRNA Knockdown Assay

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Mouse splenic DCs were isolated using MACS. Four million cells were re-suspended in 1 mL of Accell siRNA delivery medium (GE Healthcare Dharmacon) supplemented with 2.5% FBS, 1 mM sodium pyruvate and 25 mM HEPES. Cells were incubated for 72 hr with 1 µM Acell SMART pool of siRNA targeting mouse NHE1 (Slc9a1 siRNA [E-048336-00-0005], or Alpha ENaC (Scnn1a [E-040678-00-0005] GE Healthcare Dharmacon). ON-TARGETplus Non-targeting Control siRNA (D-001810-01-05) was used as a negative control. Sodium chloride (40 mM) was added for additional 24 hr. The knockdown levels of Alpha ENaC and NHE1 were analyzed by western blot.
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6

Efficient siRNA and shRNA Knockdown of VPS35

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Accell human VPS35 (55737) siRNA-SMARTpool (#E-010894-00-0010), Accell non-targeting siRNA (#D-001910-01-05), Accell siRNA delivery medium (#B-005000-100), 5× siRNA Buffer (#B-002000-UB-100) and molecular grade RNase-free water (#B-003000-WB-100) were purchased from Dharmacon. HepG2 cells were seeded in complete medium at a density of 1.5×105 cells/ml in coverslips heat-fixed on a 24-well plate. Cells were allowed to double for ∼48 h (doubling time of HepG2). After 48 h, medium was discarded, cells were rinsed with 1× PBS pH 7.4 and siRNAs were added at a final concentration of 1 μM resuspended in Accell siRNA delivery medium (#B-00-5000-100). This condition was maintained for 72 h after which the siRNA-containing medium was replaced with complete medium and again maintained for another 24 h. This ensures better knockdown at protein level. To validate knockdown of VPS35, western blotting was performed following same protocol from one well of the 24-well plate.
The lentiviral shRNA RNAi Consortium (TRC) protocol was used to produce TRC VPS35 lentiviral constructs [TRC VPS35 shRNA components (Dharmacon): RHS3979201863202, RHS3979201863553, RHS3979-201866801, RHS3979-201869452, RHS3979-201877513] (#RHS4533-EG55737) and TRC Lentiviral pLKO.1 stuffer control (#RHS4080). Knockdown of VPS35 was validated by western blotting.
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7

Silencing Polκ in DRG Neurons

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To reduce Pol κ levels in DRG neurons small interfering RNA (siRNA) was applied using the Acell system (Dharmacon Inc) designed to optimize transfection of primary cells. At 24 h after seeding siRNA was added at final concentration of 1 μM in Accell siRNA delivery medium (Dharmacon, #B-005000), and incubated for 12 h prior to the addition of 2% FBS for the duration of subsequent treatments. Transfection efficiency was assessed by imaging internalized non-targeting red fluorescent siRNA (#D-001960-01, Dharmacon) in cultures of DRG neurons and determined to be nearly 70% (supplementary Figure 1). Transfections were either with non-targeting siRNA (#D-001910-05, Dharmacon) or Pol κ targeting siRNA mixture (#A-048146-13 and #A-048146-14 Dharmacon).
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8

Targeted Silencing of mNCX-1 in Neurons

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Using the ON-targetplus SMARTpool siRNA described above, the pool of oligonucleotides were added to the cultures after a complete change from nutrient medium to 100 μl of Accell siRNA delivery medium (B-005000–500 from Dharmacon; Lafayette, CO). Preliminary experiments were conducted to determine that 100 nM to 1 μM of the siRNA produced the maximal amount of decrease in the immunoreactive area for the mNCX-1 target in neurons as determined by high content image analysis by methods to be described. For all experiments, 1 μM siRNA was used to decrease the mNCX-1 target in the DRG cultures. The progressive sequence of the siRNA treatment and response periods are shown in Figure 1. NGF (25 ng/ml) was added to the delivery medium during the 24 hour transfection period starting on day 5 after plating. After the siRNA treatment, a complete change of medium was performed to the serum-free nutrient medium containing NGF for an additional 4 days to allow time for further target silencing. Preliminary experiments were performed after the 24 hour transfection procedure to demonstrate that no toxicity was evident by the two cell viability assays employed for these studies. These same viability assays, along with image analysis of 7 neuronal parameters, were conducted on day 9 after the final mNCX-1 knockdown period.
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9

Genetic Manipulations in Cell Lines

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Retrovirus-mediated and lentivirus-mediated gene transductions were performed as described previously40 (link). To generate HT-LC3 U-2 OS and HeLa cells, cells were transduced with lentiviruses encoding HT-LC3 and selected with 1 µg/ml puromycin for 5 days. ATG2A/B double-knockout and ATG7 knockout U-2 OS cells were generated as previously described39 (link). To generate ATG13 knockout U-2 OS cells, cells were transfected with an equal amount (6 µg each per a 10-cm dish) of three human ATG13 gRNA for 48 h and sorted for GFP-positive transfected cells. Fourteen days after transfection, the cells were re-sorted for GFP-negative population to eliminate Cas9 stable transfectants and used for experiments. For siRNA screening, cells were grown overnight on the Lab-TekII 8-well Chambered Coverglass (Nunc, 155409) and incubated in Accell siRNA Delivery Medium (Dharmacon, B-005000-100) containing 1 µM Accell siRNA for 72 h. siRNA-mediated gene silencing was performed by nucleofection according to the manufacture’s protocol.
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10

Macrophage cAMP Signaling Modulation

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Human monocyte–derived macrophages were seeded onto 12-well plates at 5 × 105 cells per well and then transfected with 1 μM Accell Human Control siRNA or Accell Anti–human GPR101 siRNA SMARTpool for 72 hours in serum-free Accell siRNA Delivery Medium (Dharmacon). Cells were incubated with RvD5n-3DPA (1 nM) or vehicle (PBS containing 0.01% ethanol) for 2 minutes, after which incubations were quenched with 5% Triton X-100, cells were homogenized, and cAMP levels were determined by ELISA following the manufacturer’s instruction (Elite cAMP ELISA Assay kit, eEnzyme).
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