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6 protocols using d 001206 13 05

1

Investigating MED15 Knockdown and Metal Stress

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A549 lung adenocarcinoma cells were obtained from ATCC and maintained in Dulbecco's Modified Eagle Medium (DMEM; Gibco #11995065) supplemented with 10% fetal bovine serum (FBS; Gibco #12484028), as described [57 (link)]. The cells were seeded at a density of 5x104 cells per well in 24-well plates 24 hours before transfection. On the day of transfection, scrambled (Dharmacon #D-001206-13-05) and MED15 specific (Dharmacon #M-017015-02-0005) siRNAs were delivered into A549 cells using DharmaFECT 1 Transfection Reagent (Dharmacon #T-2001-03) according to the manufacturer’s protocol. The transfection medium was replaced with complete medium after 24 hours, and the cells were treated with 5μM CdCl2 for hours 48 hours post-transfection. MIN6 cells were cultured in 25mM glucose DMEM, as described [80 (link)], and zinc stimulation was performed by addition of 50μM ZnSO4 for 24 hours.
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2

siRNA Silencing of SOX4 in Cancer Cell Lines

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HCC38, HCC1143, and MDAMB468 cells were purchased from the American Tissue Culture Collection (Manassas, VA, USA). Cells were cultured in either RPMI-1640 medium with 10% fetal bovine serum and 1% penicillin/streptomycin (HCC38 and HCC1143) or DMEM/F12 medium with 10% fetal bovine serum and 1% penicillin/streptomycin (MDAMB468). Cells were sub-cultured at 60–70% confluence for siRNA transfections. Lipofectamine RNAiMAX (ThermoFisher) was used to transfect cells with 40nm of SMART pool siRNA targeting SOX4 (M011779010005) or scrambled control (D0012061305) according to manufacturer’s instructions (Dharmacon) for 48 hours prior to RNA or protein isolation.
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3

Silencing EIF1AX, EIF1, and EIF4B in Vero Cells

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siRNAs against EIF1AX, EIF1 and EIF4B (Smartpool M-011262-02-0005, M-015804-01-0005, L-020179-00-0005), as well as nontargeting siRNAs (Smartpool D-001206-13-05), were from Dharmacon. siRNAs were reconstituted in nuclease-free water to a concentration of 10 μM. Vero cells were plated at 1x105 cells/well of 12-well plates. The following day, 3 μl RNAiMax reagent (Thermo) was diluted in 50 μl OptiMEM and combined with 2 μl siRNA in 50 μl OptiMEM. After 5 min at RT, the reaction mix was added to cells, and media was replaced after 6 h. At 48 h post-transfection, cells were passaged and transfected again, as above. Additional DNA/RNA transfections were launched 48 h after the second siRNA transfection.
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4

MDA-MB-231 TNBC Cell Line Characterization

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The human breast cancer cell line MDA-MB-231 is a TNBC cell line originally established from the pleural effusion of a female patient with breast adenocarcinoma. The cell line was a gift from A/Prof Andreas Möller (QIMR Berghofer Medical Research Institute). The cell line was maintained in DMEM medium supplemented with 10% FBS at 37 °C in a humid atmosphere with 5% CO2 and 95% air, routinely confirmed negative for mycoplasma and bacteria contamination, and the cell line was authenticated using STR profiling. The human OTR expression plasmid (pCMV6-OTR, RC211797) and the empty vector (pCMV6-vector, PS100001) were purchased from Origene (Rockville, MD, USA). The human G-protein alpha 15 subunit (wild-type, GNA15), cloned into pcDNA3.1 (pcDNA3.1-GNA15), was obtained from the cDNA Resource Center (www.cdna.org, Bloomsberg, PA, USA). Plasmid transient transfections were carried out with FuGENE HD transfection reagent (Promega, Auburn, VIC, Australia). Selective siRNAs to knock down human OTR (M-005688-02-0005) and the control (non-targeted) siRNA (D-001206-13-05) were purchased from Dharmacon as SMARTpools. OTR knock-down transfection was carried out at a 25 nM final concentration of siRNA with DharmaFECT 1 transfection reagent (Dharmacon, Lafayette, CO, USA). The OTR overexpression and knock-down efficiency tested by qPCR are shown in Figure S1.
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5

CD11b Knockdown in Immature DCs

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Knockdown of CD11b protein with small interfering RNA (siRNA) in immature DCs was done by transfecting immature DCs at day 2 or 3 of culture with siRNA using the transfection reagent DF4 (Dharmacon) or HiPerFect (Qiagen), respectively. The transfection reagents were removed, and the cells were used for experiments 2 days after transfection. The siRNA (Smart pool; Dharmacon) was specific for CD11b (Human ITGAM M-008008-01). A nontargeting siRNA control pool (D-001206-13-05; Dharmacon) served as a control. The transfection efficiency was determined by flow cytometry of cells transfected with siGlo RISC-Free Control siRNA (D-001600-01; Dharmacon). Silencing of CD11b expression was verified by real-time PCR and flow cytometry.
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6

Slc25a1 Knockdown in Adipocytes

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For siRNA-mediated knockdown of mouse Slc25a1, siRNAs pool targeting Slc25a1 (Dharmacon, M-054849-00-0005, target sequences: 5′-GGTTTGGGATGTTCGAGTT-3′; 5′-GAAGCAGGGCTCAAACCAA-3′; 5′-GGCCAAAGGCATTCTACAA-3′; 5′-CCGAATACGTGAAGACGCA-3′) and non-targeting siRNA pool (Dharmacon, D-001206-13-05, target sequences: 5′-TAGCGACTAAACACATCAA-3′; 5′-TAAGGCTATGAAGAGATAC-3′; 5′-ATGTATTGGCCTGTATTAG-3′; 5′-ATGAACGTGAATTGCTCAA-3′) were transfected into adipocytes with the lipofectamine RNAiMAX reagent (ThermoFisher Scientific) according the manufacturer’s instruction. Forty-eight hours later, cells were harvested and subject to western blot analysis. For the rescue experiments in this study, shRNA targeting Slc25a1 lentivirus (Sigma-Aldrich, SHCLNG-NM_153150, target sequence: 5′-CTGCGGCTTGAAGATCCTAAA-3′) and non-target shRNA lentivirus (Sigma-Aldrich, SHC016, target sequence: 5′-GCGCGATAGCGCTAATAATTT-3′) were used for knockdown of Slc25a1 in stromal vascular fraction with puromycin selection followed by adipocytes differentiation.
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