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15 protocols using empty vector

1

Knockdown of Brachyury and E2F3 in Breast Cancer Cells

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MCF-7 and MDA-MB-231 (human breast cancer cell lines) were obtained from the Institute of Biochemistry and Cell Biology of the Chinese Academy of Sciences (Shanghai, China). All cells were maintained in Dulbecco's modified Eagle medium (DMEM, Thermo Fisher) supplemented with 10% fetal bovine serum (Gibco, New Zealand) and 1% penicillin/streptomycin (Invitrogen) and cultured at 37°C in a humidified incubator containing 5% CO2.
The interfering RNA (siRNA) sequences targeting Brachyury: (si-Brachyury#1)-5′-GCUGAACUCCUUGCAUAAG-3′; (si-Brachyury#2)-5′-GCUUAUCAGAACGAGGAGA-3′; the siRNA sequences targeting E2F3: (si-E2F3#1)-5′-GCGGUAUGAUACGUCUCUU-3′; (si-E2F3#2)-5′-GCAUCCACCUCAUUAAGAA-3′; the positive control siRNA: (si-GAPDH)-5′-UGACCUCAACUACAUGGUU-3′ and the negative control siRNA (si-NC)-5′-UUCUCCGAACGUGUCACGU-3′ were purchased from GenePharma (Shanghai, China). Brachyury, E2F3, and the negative control siRNAs were transfected into MCF-7 and MDA-MB-231 cells with Lipofectamine 2000 (Invitrogen, USA) according to the manufacturer's instructions. Sh-Brachyury and empty vector (GenePharma) were stably transfected into MDA-MB-231 cells. Cells were harvested for analysis at 48 h post-transfection.
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2

Transfection of shRNA, miRNAs, and Plasmids

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Short hairpin RNA (shRNA)-circ_0008043, sh-negative control (nc), mimic and inhibitor of miR-326, nc mimic and inhibitor, RAB21 overexpressing vector, and empty vector (Genepharma, Shanghai, China) were transfected into Focus and HA22T cells using Lipofectamine 3000 (Invitrogen, USA). The cells were cultured at 37°C for 48 h and qPCR was conducted to test the transfection efficiency.
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3

Lentiviral Transduction and Plasmid Transfection

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The lentiviral particles for miR-610 overexpression and inhibition constructs were parceled and bought from GeneChem (Shanghai, China). Recombinant lentivirus was adopted for infecting A375 and MV3 cells transducing units plus 5 μg /ml Polybrene (Sigma, Natick, MA, USA). Then cells were collected 48 h after transduction.
LRP6 vectors, including LRP6 expression vector, empty vector, LRP6 siRNA and control, were acquired from Genepharm Co. Ltd (Shanghai, China). The LRP6 plasmid, LRP6 siRNA and a scramble siRNA were gained from Sangon Biotech Co., Ltd. (Shanghai, China). Using six-well plate seeded cells with a concentration of 2×106 per well. Employing Lipofectamine 2000 Reagent (Invitrogen Life Technologies) transfected the treated cells with 100 nm above vectors.
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4

Modulating KISS-1 Expression in Osteosarcoma

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We induced overexpression and knockdown expression of KISS-1 mRNA in cells of the osteosarcoma cell line MG-63 in vitro, and used the same type of cells as control by transfecting them with empty vector (GenePharma, Shanghai, China). The cDNA of KISS-1 from the osteosarcoma cells was amplified by RT-PCR, and the pcDNA3.1-vector (GenePharma) was used to make constructs for eukaryotic expression using standard molecular cloning techniques. Tranfections of the MG-63 cells with KISS-1 expression vector were done using Lipofectamine (both from GenePharma), and screened by G418 (1 mg/ml). MG-63 cells with stable high expression of KISS-1 were subcultured. Additionally, a number of small interfering RNAs (siRNAs) were designed to knock down the KISS-1 expression in the MG-63 cells. The most effective siRNA segment giving the best silencing of KISS-1 expression was used in a eukaryotic expression vector pSUPER-KISS-1-siRNA, and transfected using Lipofectamine (both from GenePharma) into the cells (screened by G418 at 1 mg/ml). The MG-63 cells with stable low expression of KISS-1 were subcultured and used in subsequent experiments. The control cell line was made by transfecting the empty pcDNA3.1-vector into MG-63 cells. KISS-1 expression was verified by RT-PCR method in all the resulting cell lines.
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5

Lentiviral Transduction of DDR1 and COL4A1 Silencing in RT4 Cells

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lentiviral vectors expressing GFP were purchased from Genechem (Shanghai, China). The full-length human DDR1 coding sequences were obtained by PCR amplification and then accurately cloned to the lentiviral vector (Genechem, Shanghai, China). Using Lipofectamine 2000 (Invitrogen), the recombinant lentiviral vector was transfected into HEK293 T cells (Lentivirus-DDR1) for 48 h, followed by infection with RT4 cells. The stably transfected RT4 cells were screened using culture medium containing 6 μg/mL puromycin (Sigma, USA). RT4 cells transfected with the empty vector (GenePharma, Shanghai, China) were designed as a negative control (RT4-NC). The GFP density imparted by the lentiviruses was utilized to detect transfection efficiency. In addition, COL4A1-specific siRNA and the control siRNA were synthesized by Sangon Biotech (Shanghai) Co., Ltd. and transfected into cells using Lipofectamine 2000 (Invitrogen) to inhibit COL4A1 in cells.
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6

Overexpression and Knockdown of E2F1

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RPL5 overexpressing vector, E2F1 overexpressing vector, E2F1-specific siRNAs, empty vector, and siRNA were purchased from GenePharm, Shanghai. MCF-7 cells were seeded into 6-well plates and transfection was conducted with Lipofectamine 3000 (Invitrogen) following the manufacturer’s protocol for 48 h.
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7

LUNAR1 Silencing and IGF-1R Overexpression in Colorectal Cancer

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Colorectal cancer cell lines utilized in the present study are HT29, SW480 and SW620, which was purchased from the Chinese Academy of Sciences Cell Bank (Shanghai, China). According to the instructions for these cell lines, the cells were cultured in L-15 or 1640 medium (Invitrogen, Carlsbad, CA) supplemented with 10% foetal calf serum. To downregulate LUNAR1 expression in cells, LUNAR1 targeted stealth RNAi (LUNAR1 siRNA) was utilized (Invitrogen, Carlsbad, USA). The sequence of the LUNAR1-targeted small interfering RNA was GATTCTGTAGCCTAACAAGCTTTCCAGTGATT. During transfection, according to the manufacturer’s instructions, the cells were transfected with 50 nmol of LUNAR1 siRNA using Lipofectamine 2000 transfection reagent (Invitrogen, Carlsbad, USA) with a scrambled negative control. After transfection of LUNAR1 siRNA, cells were also transfected with plasmids containing IGF-1R (pcDNA3.1-IGF1R) and empty vector (GenePharma, Shanghai, China). The transfected cells were harvested after 48 h of incubation for real-time PCR investigation to evaluate the transfection efficiency and target gene expression.
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8

Optimizing BMSC Transfection for Wnt3a Silencing

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BMSCs were transfected with a multiplicity of infection (MOI) of 25, 50, 100, and 200 respectively, and 200 was found to be the best MOI. BMSCs in good condition were selected and inoculated on 24-well plates at a density of 1x104 cells/well and incubated overnight at 37˚C. After 24 h, recombinant LV-small interfering (si)RNA-Wnt3a-mus (forward: AGTGCCTCGGAGATGGTGGTAG; reverse: GGGTTAGGTTCGCAGAAGTTGGG) lentivirus (GenePharma Co., Ltd.) or empty vector (GenePharma Co., Ltd.) lentivirus was added to the medium at a multiplicity of infection of 200 (MOI=200). The normal group was cultured with complete medium without adding lentivirus. After 96 h of infection, green fluorescent protein (GFP) was observed at x400 under an inverted fluorescence microscope (Olympus Corporation). Two groups were used: IGF-1 + EV (empty vector) and IGF-1 + siRNA-Wnt3a.
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9

Stable BMP2 Overexpression in S18 and 6-10B Cells

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For BMP2 overexpression study, S18 and 6-10B cells stably expressing BMP2 were obtained by infecting with BMP2 expression lentiviral vector (GenePharma, Shanghai, China) and selecting with 2 μg/mL puromycin for 2 weeks according to the manufacturer's instructions. So as the control cells infecting with empty vector (GenePharma, Shanghai, China).
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10

Functional Validation of m6A Regulators in BMSCs

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short hairpin RNA (Sh)-METTL14, sh-YTHDF1, sh-YTHDF2, sh-YTHDC1, sh-IGF2BP1, sh-IGF2BP2, sh-IGF2BP3, sh-NC, empty vector, and SMAD1 overexpression vector, IGF2BP1 overexpression vector, and IGF2BP2 overexpression vector were obtained from Genepharma. BMSCs were seeded into 6-well plates and transfected with sh-METTL14 and sh-NC using Lipofectamine 3000 (Invitrogen, Carlsbad) for 48 h.
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