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9 protocols using opi mem

1

siRNA Transfection Optimization Protocol

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For transfection of siRNA, cells were plated at a density of 1×105 cells per well in 6-well plates, cell density was ~60–80% per well. Then cells were transfected with negative control (NC), or specific siRNAs for HDAC7, NudCD1 and GGH (100 nM; Shanghai GenePharma Co., Ltd.), respectively, using Lipofectamine® RNAiMAX transfection reagent (Invitrogen; Thermo Fisher Scientific, Inc.). For transfection, 125 µl opi-MEM (Thermo Fisher Scientific) was mixed with 25 pmol siRNA and another 125 µl opi-MEM was mixed with 7.5 µl RNAiMAX and the mixture was incubated at room temperature for 15 min respectively. Then the iMAX solution was added to the siRNA solution, mixed well and incubated at room temperature for another 15 min. Finally, the 250 µl mixture was added into indicated wells. After transfection of 24 h, the culture medium was aspirated and replaced with new complete medium for another 24 h.
The siRNA sequences were: HDAC7: 5′-ACUUCUUGGGCUUAUAGCGCA-3′, 5′-CGCUAUAAGCCCAAGAAGUCC-3′; NUDCD1: 5′-AGUGUAUAUUGAUCAUCUCGA-3′, 5′-GAGAUGAUCAAUAUACACUGG-3′; GGH: 5′-UUUUUGCAUUAAUAUUCCGAU-3′, 5′-CGGAAUAUUAAUGCAAAAAUG-3′; NC: 5′-UUCUCCGAACGUGUGACGUTT-3′, 5′-ACGUGACACGUUCGGAGAATT-3′.
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2

Lipofectamine-mediated siRNA Transfection

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Cells were seeded into 6-well plates at the density of 1 × 105 cells/well and transfected using the 5 μl Lipofectamine 2000 (Life Technologies, USA), which was mixed with 2 μl of 20 μM siRNA in 250 μl of Opi-MEM (Gibco, USA). The siRNAs/antisense oligonucleotides (ASOs) were obtained from GenePharma Ltd. (Suzhou, China).
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3

Heterologous Expression of TRP Channels

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HEK293T, N2a, HeLa and CHO cells were used for heterologous expression of TRP channels. Cells were grown in Dulbecco's modified Eagle medium (DMEM) with 10% FBS, then transferred on 2 ml Petri dishes for transfection. Lipofectamine 3000 Transfection Reagent (Thermo Fisher Scientific) kit was used according to manufacturer instructions: 1–3 μg of plasmid (Table S1), 5 μl of Lipofectamine 3000, and 5 μl of P3000 were mixed in 250 μl Opi-MEM (Gibco) for 5 min and then added to cells for 24 h incubation. Some plasmids were mixed with 0.5 μg GFP (pIRES2-EGFP) to enable selection of transfected cells. The surface-expressing TRPML1 mutant TRPML1-L15L/AA-L577L/AA (4A) was used for patch clamp recordings. All plasmids were verified by Sanger Sequencing.
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4

Lentiviral Knockdown in MCF-7 and 293T Cells

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MCF-7 breast cancer cell strains and 293T cells were purchased from the Shanghai Cell Resource Center of the Chinese Academy of Sciences (Shanghai, China). The pSPAX2, pMD2G and pLVX-shRNA1 vectors were purchased from Clontech Laboratories (Mountain View, CA, USA). The Plasmid Midi kit was purchased from Qiagen (Valencia, CA, USA). Opi-MEM, Escherichia coli DH5α and Taq DNA polymerase were purchased from Invitrogen Life Technologies (Carlsbad, CA, USA). T4 DNA ligase, BamHI and EcoRI restriction enzymes were purchased from New England Biolabs (Ipswich, MA, USA). Liposome Lipfectamine 2000, Dulbecco’s modified Eagle’s medium (DMEM), fetal bovine serum (FBS) and Trypsin were purchased from Invitrogen Life Technologies. The gel extraction kit was purchased from Tiangen Biotech (Beijing) Co., Ltd. (Beijing, Japan). KOD high fidelity enzyme polymerase chain reaction (PCR) kit and Taq enzymes were purchased from Toyobo Co., Ltd. (Osaka, Japan). DNA ladder was purchased from Fermentas International, Inc., (Burlington, Canada). The Transwell chamber was purchased from Chemicon (Temecula, CA, USA).
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5

Reprogramming Fibroblasts to hiPSCs

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To prepare the retroviruses, HEK 293T cells were transfected with pMXs plasmids containing the coding sequences for SOX2, OCT3/4, and KLF4, along with pUMVC and pCMV-VSV-G plasmids at the ratio of 10 ug of plasmid DNA to 20 µl of Fugene 6 (Roche) in 500µl Opi-MEM (Invitrogen). The ratio of pMXs:pUMVC:pCMV-VSV-G was 3:2:1. Next day, the culture medium containing the retroviruses was harvested and concentrated by Retro-X™ Concentrator (TAKARA). The human fibroblasts were plated at 1×105 cells per well in the 6-well plate one day before infecting with the retroviruses. The retrovirus solution was added to the fibroblasts and incubated overnight. 24 hours after the infection, infected fibroblasts were plated in gelatin-coated 100mm dishes containing irradiated feeder cells. One day after plating on feeder cells, the medium was changed to hESC culture medium. hESC-like clones were observed 25–30 days after the initial infection. The hiPSC clones were picked up around 45 days after the initial infection. 8 lines of hiPSC were established from 8 different donors and used in the subsequent experiments.
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6

Transfection of EMSCs with siRNA

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The 3rd generation E19.5d EMSCs were plated onto 6-well plates at 70–90% confluence and were cultured for 24 h. Two hours before transfection, the culture medium was changed to DMEM/F12 (without penicillin, streptomycin, and FBS). siRNA-LNGFR and siRNA-NC (GenePharma, Shanghai, China) were transfected into E19.5d EMSCs using Lipofectamine 2000 in OPI-MEM (Invitrogen, Carlsbad, CA, USA). The siRNA sequences are listed in Supplementary Table S2.
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7

Reprogramming Fibroblasts to hiPSCs

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To prepare the retroviruses, HEK 293T cells were transfected with pMXs plasmids containing the coding sequences for SOX2, OCT3/4, and KLF4, along with pUMVC and pCMV-VSV-G plasmids at the ratio of 10 ug of plasmid DNA to 20 µl of Fugene 6 (Roche) in 500µl Opi-MEM (Invitrogen). The ratio of pMXs:pUMVC:pCMV-VSV-G was 3:2:1. Next day, the culture medium containing the retroviruses was harvested and concentrated by Retro-X™ Concentrator (TAKARA). The human fibroblasts were plated at 1×105 cells per well in the 6-well plate one day before infecting with the retroviruses. The retrovirus solution was added to the fibroblasts and incubated overnight. 24 hours after the infection, infected fibroblasts were plated in gelatin-coated 100mm dishes containing irradiated feeder cells. One day after plating on feeder cells, the medium was changed to hESC culture medium. hESC-like clones were observed 25–30 days after the initial infection. The hiPSC clones were picked up around 45 days after the initial infection. 8 lines of hiPSC were established from 8 different donors and used in the subsequent experiments.
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8

Transfection of HEK293 cells with KV1.3 plasmid

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HEK293 cells were seeded in 6-well plates at a density of 0.6 × 106/well and, grew overnight to reach 70–90% confluent. Lipofectamine 2000 reagent was diluted in Opi-MEM (Invitrogen) at a ratio 5 µl: 95 µl. The pJK or pJK/KV1.3 plasmid at amount of 2.5 µg was diluted in Opi-MEM to make the final volume at 100 µl. Diluted plasmids were added to each tube of diluted lipofectamine 2000 and, incubated at room temperature for 15 min. DNA-lipofectamine complex were applied to cells. Cells were collected and lysed after 48 h. The pJK and pJK/KV1.3 plasmids were gifts provided by Professor Erich Gulbins from Department of Molecular Biology, University of Duisburg-Essen, Essen, Germany (Szabo et al., 2005 (link)).
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9

siRNA and miRNA Transfection in U87 Cells

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U87 cells were seeded in 12-well plates and transfected with siRNAs or miRNAs for 48 h using Opi-MEM and lipofectamine RNAiMAX (catalog #13778150; Thermo Fisher Scientific). The siRNA against SLC7A11, its control siRNA, miR-18a mimic, and mimic-negative control were synthesized and purified by Sango Biotech. Sequences are shown in Table S5.
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