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9 protocols using on targetplus smartpool small interfering rna sirna

1

Transfection of siRNA and Expression Vectors in MDMs and HeLa Cells

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100 nM scrambled or ON-TARGETplus SMARTpool small interfering RNA (siRNA) against the indicated genes (Dharmacon, Lafayette, CO) (four pooled siRNAs for each gene) was transfected into MDMs using nucleofector (Amaxa, San Diego, CA) for 48 hours. Three micrograms (for MDMs) or 4 µg (for HeLa cells) empty vector (pcDNA3.0), FLAG-IL23R/R381 or FLAG-IL23R/Q381 (generated from IL23R cDNA (OriGene, Rockville, MD)) through mutagenesis (QuikChange Lightning Kit; Agilent Technologies) ±IL12Rβ1 (GeneCopoeia, Rockville, MD) was transfected into MDMs by nucleofector or into HeLa cells by Lipofectamine 2000 (Invitrogen).
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2

Knockdown of IDO in Mesenchymal Stem Cells

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To knock down IDO, the ON-TARGETplus SMART-pool small interfering RNA (siRNA) (L-010337-01-0005; GE Dharmacon, Lafayette, CO, USA) was used. The sequences were as follows: Human IDO1, NM_002164, sense, 5′-UCACCAAAUCCACGAUCAUUU-3′, antisense, 5′-PUAUGCGAAGAACACUGAAAUU-3′; sense, 5′-UUUCAGUGUUCUUCGCAUAUU-3′, antisense, 5′-PUAUGCGAAGAACACUGAAAUU-3′; sense, 5′-GUAUGAAGGGUUCUGGGAAUU-3′, antisense, 5′-PUUCCCAGAACCCUUCAUACUU-3′; and sense, 5′-GAACGGGACACUUUGCUAAUU-3′, antisense, 5′-PUUAGCAAAGUGUCCCGUUCUU-3′. The ON-TARGETplus siCONTROL Nontargeting Pool (D-001810-10-05; GE Dharmacon) was used as the negative control. siRNAs were transfected into MSCs by the Amaxa Nucleofector II device (Lonza) and the Human MSC Nucleofector kit (Lonza). Briefly, aliquots of 5 × 105 MSCs were re-suspended in 100 μl of the Nucleofector solution in the presence of 1.5 μg of IDO or control siRNA and then electroporated by the U-23 program. Cells were immediately transferred into 37 °C pre-warmed complete culture medium and plated onto six-well dishes. After 72 h from transfection, cells were harvested and lysed for the immunoblotting measurement of IDO levels, while the supernatants were recovered for the assessment of IDO activity and to be used in functional assays.
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3

RNAi-mediated Histamine Receptor Regulation

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For RNAi assays, H1R or H2R On-Target plus Smart pool small interfering RNA (siRNA; Dharmacon) or negative control siRNA (50 nM) were delivered using the DharmaFECT transfection reagent as recommended by the manufacturer. At 48 h post-transfection, the cells were induced by Dox (0.5 μg/mL) in combination with histamine (100 μM) for additional 48 h, then protein expression was measured by Western blot.
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4

siRNA Knockdown of NLRP3, EP2, EP4, and cPLA2α

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ON-TARGETplus SMART pool small interfering RNA (siRNA) (Dharmacon, Thermo Scientific, Lafayette, CO) against human NLRP3 (L-017367-00-0005), or sc-45469, Santa Cruz), EP2 (PTGER2) (L-005712-00-0005), EP4 (PTGER4) (L-005714-00-0005) and cPLA2α (PLA2G4A) (L-009886-00-005) together with ON-TARGETplus Control Non-targeting pool (D-00181970-05) were used to perform knockdown experiments in human primary MDM or THP-1 cells. Human primary MDM (0.5×106 cells per 100 μl cuvette) or THP-1 cells (5×106 per 100 μl cuvette) were transfected with siRNA pools (1 μM or 100 nM) using a P3 Primary Cell 4D-Nucleofector X Kit L (Amaxa, Cologne, Germany) according to the manufacturer's protocols for human macrophages and monocytes, respectively. The silencing of gene expression was confirmed by RT-PCR. All experiments on transfected cells were performed after 48 hours.
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5

Modulating miR-204-5p Expression in Hippocampal Cells

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ON-TARGET plus SMART pool small interfering RNA (siRNA) against mouse miR-204-5p and ON-TARGET plus non-targeting siRNA pool were purchased from Dharmacon. The TransIT-X2 Dynamic Delivery System (Mirus Corp., Madison, WI, USA) was used for siRNA transfection, as described by the manufacturer. In corticosterone treatment and miR-204-5p knockdown experiments, the mHippoE-14 cells in 6-well plates were transfected with 30 nM miR-204-5p siRNA or control siRNA. After 2 h transfection, cells were treated with 100 ng/mL corticosterone (Sigma Chemical Co., St. Lous, Mo, USA) or ethanol for 72 h. In flutamide treatment and miR-204-5p knockdown experiments, the mHippoE-14 cells in 6-well plates were treated with 1 μM flutamide for 48 h and then were transfected with 30 nM miR-204-5p siRNA or control siRNA for 24 h.
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6

Knockdown of TGF-β Pathway Signaling

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To knock down endogenous ALK4, ALK5, ALK7, SMAD2, SMAD3, and SMAD4, the cells were transfected with 50 nM ON-TARGETplus SMARTpool small interfering RNA (siRNA) (Dharmacon, Lafayette, CO) using Lipofectamine RNAiMAX (Invitrogen, Life Technologies). The siControl non-targeting pool siRNA (Dharmacon) was used as the transfection control. The knockdown efficiency was determined by RT-qPCR and western blotting.
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7

Silencing TRIM25 in Lung Cancer Cells

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Cells were seeded into 6-well plates at 2 Â 10 5 cells per well, grown for 24 hours in complete medium, and then transfected with ON-TARGET plus Smart pool small interfering RNA (siRNA) specific to TRIM25 or scrambled siRNA-negative control (Dharmacon, Chicago, Illinois) at a final concentration of 100 nmol/L using Hyperfect transfection reagent (Qiagen, Courtaboeuf Cedex, France) according to the manufacturer's directions. Note that 2 different siRNAs against nonoverlapping messenger RNA (mRNA) sequence of TRIM25 were applied. To examine RNAi efficiency, cells were harvested 2 days after siRNA transfection and analyzed by Western blots. For establishment of TRIM25 stable knockdown cell lines, retroviral construct containing pSuper with short hairpin RNA (shRNA) against human TRIM25 and pSuper were prepared as described previously. The generation of retrovirus supernatants and transfection of lung cancer cells were conducted as described previously. The expression of TRIM25 was confirmed by Western blotting analysis.
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8

Targeted Knockdown of Key Oncogenes in CRC Cells

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CRC cell lines were seeded in six-well plates (see Supplementary Table S1 for the number of plated cells) and transfected after approximately 16 hours, using Lipofectamine RNAiMAX (Invitrogen, Thermo Fisher Scientific) in reduced-serum Opti-MEM medium (Gibco, Thermo Fisher Scientific). Gene silencing was achieved with ON-TARGETplus SMARTpool small interfering RNA (siRNA) specific for KRAS (L-005069-00-0010), C-MET (L-003156-00-0005) and HER3 (L-003127-00-0005) at a final concentration of 10 nM, and PIK3CA (L-003018-00-0010) at a final concentration of 50 nM, all from Dharmacon. As a negative control (siCTRL), a nontargeting siRNA (D-001810-01-50; ON-TARGETplus Non-targeting siRNA #1) was used. Subsequent assays were performed upon 72 hours of cell transfection for KRAS, C-MET and PIK3CA and 48 hours for HER3. Silencing efficiency was monitored by western blot.
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9

Studying SK1, S1PR1, and S1PR3 roles

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HmSMC were transfected with human SK1 (L-004172), S1PR1 (L-003655), S1PR3 (L-005208) or control (L-005361) ON-TARGETplus SMARTpool small interfering RNA (siRNA) (100 nM final concentration) (Dharmacon, Waltham, MA) using OptiMEM (Invitrogen/Life Technologies, Saint Aubin, France) and HiPerFect reagent according to the manufacturer's recommendations (Qiagen, Courtaboeuf, France).
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