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4 protocols using scrambled oligonucleotides nc

1

Cell culture and transfection of OSCC

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Human OSCC cell lines, including SCC-4, Tca8113 and SCC-9, and human normal oral keratinocyte NOK cell line were purchased from the Cell Bank of the Chinese Academy of Sciences (Shanghai, China). These cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; Hyclone, Logan, UT, USA) containing 10% fetal bovine serum (FBS; Sigma-Aldrich, St. Louis, MO, USA), 100 U/mL penicillin and 100 μg/mL streptomycin at 37°C in a humidified incubator with 5% CO2.
The specific small interference RNA (siRNA) targeting HCP5 (si-HCP5), miR-140-5p mimics and the scrambled oligonucleotides (NC) were obtained from GenePharma Co., Ltd (Shanghai, China). The full length sequence of human HCP5 cDNA was amplified by PCR, and then subcloned into the vector pcDNA3.1 (Invitrogen, Carlsbad, CA, USA). Cells grown at 70–80% confluence were transfected with the oligonucleotides and vectors using Lipofectamine 2000 (Invitrogen). After 48 hrs, the cells were collected for further experiments.
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2

Targeting TTN-AS1 with siRNA

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The small interfering RNA (siRNA) targeting TTN-AS1 (si-TTN-AS1), siRNA negative control (si-NC), miR-195 mimics, and scrambled oligonucleotides (NC) were all obtained from Shanghai GenePharma Co., Ltd. (Shanghai, China). The cDNA encoding TTN-AS1 was amplified by PCR, and then ligated into pcDNA3.1 ( + ) vector (Invitrogen). Cell transfection was performed using Lipofectamine 2000 (Invitrogen). After 48 h, the transfection efficiency was validated by RT-qPCR analysis.
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3

TMPO-AS1 Regulation in Gastric Cancer Cells

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Four GC cell lines (HGC-27, SGC-7901, BGC-823 and AGS) and one normal human gastric mucosa cell line GES-1 were obtained from the Cell Bank of Chinese Academy of Sciences (Shanghai, China). These cell lines were cultured in RPMI-1640 medium (Invitrogen, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (FBS; HyClone, Logan, UT, USA) and 1% penicillin-streptomycin at 37°C in a humidified atmosphere containing 5% CO2.
si-TMPO-AS1, pcDNA3.1-TMPO-AS1, miR-140-5p mimics, the scrambled oligonucleotides (NC) and empty pcDNA3.1 vector were obtained from Shanghai GenePharma Co., Ltd. (Shanghai, China). To perform transfection, cells were cultured to about 70–80% confluence. Then, Lipofectamine 3000 Transfection Reagent (Invitrogen) was used. After 48 h, the transfection efficiency was validated by RT-qPCR analysis.
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4

Lentiviral Knockdown and Overexpression of XIST and EZH2

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Lentivirus particles expressing short hairpin RNA (shRNA) targeting XIST or scrambled oligonucleotides (NC) were purchased from GenePharma (Shanghai, China). The KYSE30 and KYSE150 cells were transfected with lentivirus. At 48h after transfection, cells were treated with puromycin (3μg/ml) for 7 days and the transfection efficiency was determined by GFP-positive cell percentage.
The miR-101 mimic, miR-101 inhibitor and negative control (miR-NC) were obtained from Ribobio (Guangzhou, China). To restore EZH2 expression, a pcDNA3.1-EZH2 plasmid, which contained the coding sequences but lacked the 3'-UTR of EZH2 was constructed. The cell transfection was performed with Lipofectamine2000 according to the manufacturer's instructions. Briefly, cells were placed in a 6-well plate the day before transfection. At 48h after transfection, cells were collected for subsequent analysis or subjected to qRT-PCR and western blot assays to confirm the transfection efficiency.
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