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26 protocols using si nc

1

Silencing ADAMTS9-AS1 in Glioma Cells

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Human glioma cell lines (U251 and U87) and normal human astrocytes (NHAs) were obtained from the American Type Culture Collection (ATCC, Manassas, VA, USA). All cell lines were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM, Gibco, NY, USA) that was supplemented with 10% fetal bovine serum (FBS, Gibco), maintained at 37°C in a humidified incubator with 5% CO2.
Small interfering RNAs (siRNAs) targeting ADAMTS9-AS1 (si-ADAMTS9-AS1#1: 5′-ACAGCTATATCAGCCAACCAGAGT-3′′ and si-ADAMTS9-AS1#2: 5′-ACCAGCCAGAGCAAGCTATATACT-3′), as well as a negative control (si-NC: 5′-GTTTACAACACGCTTCCTCTGA-3′) were purchased from Santa Cruz Biotechnology Inc. (Dallas, TX, USA). U251 and U87 cells were plated in 6-well plates at a density of 1 × 105 cells per well and grown to reach 70-80% confluency, followed by a transfection with si-ADAMTS9-AS1#1, si-ADAMTS9-AS1#2, or si-NC for 48 h with lipofectamine 2000 Reagent (Invitrogen, Carlsbad, CA, USA) complied with manufacturer’s instruction.
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2

SELENOT Knockdown in H9c2 Cardiomyocytes

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SELENOT gene silencing in H9c2 cardiomyocytes was performed as previously described by Rocca et al. (2022) [16 (link)]. Briefly, H9c2 cardiomyocytes (5000 per well) were seeded in 96-well plates and incubated for 48 h at 37 °C, 5% CO2. SELENOT siRNA (100 nmol/L) was transfected into H9c2 cardiomyocytes in serum-free medium using the Lipofectamine 2000 transfection reagent following the manufacturer’s instructions (Invitrogen, Thermo Fisher Scientific, Waltham, MA, USA). Negative control si-RNA (si-NC) was used to detect non-specific effects of siRNA delivery and to compare siRNA-treated samples. Both si-NC and siRNA for SELENOT were purchased from Santa Cruz Biotechnology. H9c2 cardiomyocytes were transfected in serum-free medium for 6 h, after which the medium was replaced with full-medium and cells were incubated for 36 h at 37 °C, 5% CO2. H9c2 cells were treated with PA (100 µmol/L) or co-treated with PA and increasing concentrations of PSELT (from 5 to 100 nmol/L) for 24 h. At the end of the treatments, the viability of the H9c2 cells was evaluated by MTT assay. The cell viability was reported as the percentage cell survival relative to the si-NC transfected cells in six wells for each experimental group [16 (link)]. The experiment was repeated three independent times.
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3

siRNA Knockdown of Proliferation Genes

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Short interfering RNA (siRNA) against KIF20A, CCNB2 and CDCA8 (si-KIF20A, si-CCNB2 and si-CDCA8), and negative control siRNA with nonspecific sequences (si-NC) were purchased from Santa Cruz Biotechnology (Santa Cruz, CA, USA). For cell transfection, an equal dose (40 pmol) of si-KIF20A, si-CCNB2, si-CDCA8, or si-NC was transiently transfected into 786-O cells, which were seeded in six-well plates. The cells were employed in in-vitro loss-of function assays 48 hafter transfection.
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4

Silencing Sirt3 in HK-2 Cells

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Sirt3 (si-Sirt3; GenePharma, Shanghai, China) or negative control- (si-NC; Santa Cruz Biotechnology, Santa Cruz, CA, USA) specific small interfering RNA (siRNA) was transfected into HK-2 cells. The efficiency of silencing Sirt3 after transfection was determined by western blotting experiments.
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5

FOXC1 Knockdown in Pancreatic Cancer Cells

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A FOXC1-specific siRNA (si-FOXC1) and its non-specific scramble siRNA (si-NC) were purchased from Stanta Cruz (Santa Cruz Biotechnology, USA), and transfections were carried out with Lipofectamine 2000 according to manufacturer’s recommended protocol. Briefly, Capan-2 and PANC-1 cells were transfected with either si-FOXC1 (100 nM) or si-NC (100 nM) for 48 h, followed by examination of cell proliferation. The efficiency of the siRNA on knocking down FOXC1 expression was examined by qRT-PCR 48 h after transfection.
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6

Knockdown of PGC-1α and Nrf2 in H9c2 Cells

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The small interfering RNA (siRNA) duplexes corresponding to rat PGC-1α (siPGC-1α), Nrf2 (siNrf2) and the negative control siRNA (siNC) were purchased from Santa Cruz Biotechnology, Inc. siRNAs (100 nM) were transfected into H9c2 cells using Lipofectamine® 2000 reagent (Thermo Fisher Scientific, Inc.), according to the manufacturer’s instructions. In brief, H9c2 cells (5×105) were plated in a 6-well plate and cultured for 24 h. When the cells reached 80% confluence, Lipofectamine 2000 was added to the medium without serum and incubated for 5 min at room temperature. The diluted siRNA was gently mixed with the medium containing Lipofectamine 2000 and incubated for 20 min at room temperature prior to adding the mixture to each well containing cells and medium. The transfected cells were cultured at 37°C in a CO2 incubator for 24 h prior to subsequent experiments. Untransfected cells were used as a blank control, and cells transfected with siNC were used as a negative control.
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7

Silencing Key Regulators in Endothelial Cells

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HUVECs and EPCs were obtained from Yale VBT core, Yale School of Medicine and grown in EGM-2 BulletKit (CC-3162, Lonza). For the siRNA treatment assay, cells were cultured at 60–70% confluence in six-well plates and transferred with total 30 pmol siCCM3 (sc-62084, Santa Cruz), siATPIF1 (sc-78711, Santa Cruz), siS100A11 (sc-60314, Santa Cruz) or siNC (sc-37007, Santa Cruz) using Lipofectamine RNAiMAX Transfection Reagent (13,778,150, Invitrogen), according to the manufacture’s instruction. Cells were cultured 48 h before harvest. For the MG132 treatment, cells were incubated with 10 μm MG132 or the same volume of DMSO as negative control for 12 h before harvest.
For EdU staining, siRNA and pLEX-ATPIF1 treated HUVECs were stained with EdU (Click-iT® EdU Imaging Kits, C10337) according to the manufacture’s instruction.
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8

Silencing Target Genes in BMDM Cells

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SiRNAs of the target genes, including siTNFAIP3 (Cat# sc-37656), siSTAT3 (Cat# sc-29494), siCD36 (Cat# sc-37245), siABCG1 (Cat# sc-41139), and the corresponding negative control RNAs (si-NC) were purchased from Santa Cruz Biotechnologies. Transient transfection of these siRNAs into BMDM cells was performed using Lipofectamine™ RNAiMAX Transfection Reagent (Cat# 13778075, Invitrogen, Carlsbad, CA, USA) according to manufacturer’s instructions. Macrophages were transfected with 20 nM siRNA and the cells were used for analysis after 24–48 h of transfection.
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9

Ferrochelatase knockdown in T24 and MGH-U3 cells

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T24 and MGH-U3 cells in 6-well plates at 1×105 cells/well were transfected with synthesized siRNA ferrochelatase (si-FECH; cat. no. sc-60631; Santa Cruz Biotechnology, Inc.) or siRNA negative control (si-NC; cat. no. 4390843; Invitrogen; Life Technologies; Thermo Fisher Scientific, Inc.) with 50 pmol of siRNA and 5 µl of Lipofectamine 2000 (Life Technologies; Thermo Fisher Scientific, Inc.) in 6-well plates according to the manufacturer's instructions at 37°C for 48 h. Following transfection, protein was extracted, and the expression of ferrochelatase was measured in each cell line by western blotting.
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10

Modulating miR-145 and AFAP1-AS1 in SCC9 Cells

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The miR-145 mimics (5′-GUCCAGUUUUCCCAGGAAUCCCU-3′), miR-145 inhibitor (anti-miR-145; 5′-AGGGAUUCCUCCCAAAACUGGAC-3′), mimics negative control (miR-NC; 5′-GUAGGAGUAGUGAAAGGCC-3′) and inhibitor NC (anti-miR-NC; 5′-GGCCUUUCACUACUCCUAC-3′) were purchased from Guangzhou RiboBio Co., Ltd. Two small interfering RNAs (siRNA/si) targeting AFAP1-AS1 (si-AFAP1-AS1#1; 5′-GGACCATTTGGTGTATCTTT-3′ and si-AFAP1-AS1#2; 5′-GGTGGAGAATGAACATTCUTT-3′) and the corresponding control scramble NC (si-NC; 5′-TTCTCCGAACGTGTCACGTTT-3′) were purchased from Santa Cruz Biotechnology, Inc. Short hairpin RNA (shRNA/sh) targeting AFAP1-AS1 (sh-AFAP1-AS1; 5′-TTATTTTGCTAATTCAAC-3′) and the corresponding control (sh-NC; 5′-CCTAACCACAAACTCTACGGC-3) were synthesized and packaged in lentiviral vectors (Lv) by Shanghai GenePharma Co., Ltd. SCC9 cells were transfected with each transfectant (600 ng) using 3 µl Lipofectamine® 2000 reagent (Invitrogen; Thermo Fisher Scientific, Inc.) according to the manufacturer's protocol. Following incubation at 37°C for 6 h, the serum-free DMEM medium was replaced with fresh RPMI-1640 medium containing 10% FBS, and then cells were cultured for 24–72 h for further assays.
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