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17 protocols using dharmafect 2 reagent

1

Piwi4-mediated Host Transcriptome Regulation During ASALV Infection

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A total of 2.5 × 105 AF5 cells/well were seeded into 24-well plates the day before transfection with 200 ng of gene-specific dsRNAs or control dsRNA (dsLacZ) per well and transfected using 1 μL of Dharmafect2 reagent (GE Dharmacon). For siRNA knockdowns in knockout cells, 20 nM either Piwi4-specific siRNAs or control siRNA (Horizon Discovery) was transfected using 2 μL Dharmafect2 reagent (GE Dharmacon), as previously described (18 (link)). The following day, ASALV infection (MOI of 0.5) was performed. At 48 hpi, total RNA was isolated from cells using TRIzol (Ambion). cDNA of 1.5 μg RNA was produced using Moloney murine leukemia virus (M-MLV) reverse transcriptase (Promega) and oligo(dT)15 primers (Thermo Fisher Scientific) according to the manufacturers’ protocols. SYBR green qRT-PCR for mRNA targets was performed using gene-specific primers (Table S1) and ribosomal protein S7 RNA as the housekeeping gene transcript. Results were analyzed using the 2−ΔΔCT method with LacZ dsRNA samples as the control. All qPCRs were performed in technical triplicates.
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2

Culturing and Transfecting ATII Cells

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ATII (alveolar epithelial type II, kindly provided by Prof Julian Downward, The Francis Crick Institute, UK) cells (18 (link)–21 (link)) were cultured in DCCM-1 (Biological Industries Ltd) supplemented with 10% new-born calf serum (NBCS) (Life Technologies), 1% penicillin, 1% streptomycin, and 1% L-glutamine (all from Life Technologies). All cells were kept at 37°C and 5% CO2. No mycoplasma contamination was detected in the cell lines used.
Short interfering RNA (siRNA) oligos against GRK6 or control siRNA were purchased from Biomics Biotechnologies Co., Ltd, China. Sequences are available from an earlier publication (17 (link)). Cells were transfected with the indicated siRNA oligos at a final concentration of 35 nM using Dharmafect 2 reagent (Dharmacon).
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3

RNA Interference Using DharmaFECT 2

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RNA interference was carried out using DharmaFECT 2 reagent (Dharmacon, Lafayette, CO, USA) according to manufacturer’s instructions. Validated pools of EDIL3-siRNA and non-targeting siRNA as negative control were ordered from Dharmacon (ON-TARGETplus SMART pools L-017593 and D-001810) and used at 50 nM. Cells were subjected to drug treatments 24 h after RNA interference.
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4

Optimized siRNA-Mediated Knockdown Protocol

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Cells were seeded in 24-well plates 48 hours before siRNA transfection in order to have 60–70% confluency on the day of transfection. Cells were transfected with siRNA (Dharmacon) targeting (ATF4 and DDIT3) and control siRNA at a final concentration of 100 nM using DharmaFECT 2 reagent (Dharmacon). ON-TARGET plus siRNA pool (Dharmacon) was used for all knockdown experiments because it contains a pool of four individual siRNA sequences for the target gene. RNA knockdown was confirmed by assessing mRNA levels with qRT-PCR.
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5

STAT1 Silencing in MDA-231 Cells

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STAT1 was silenced in MDA-231 cells by using small interfering RNA (siRNA) at 5 µM (STAT1-RNAi sense 5′-(P)CUACGAACAUGACCCUAUCUU-3′, anti-sense 5′-(P)GAUAGGGU CAUGUUCGUAGUU-3′, Dharmacon, Thermofisher Scientific) transfected with Dharmafect2 reagent according to the manufacturer' instructions. siGenome non-targeting RNApool2 (Dharmacon) served as controls at the same concentration. Proteins were extracted after 48 h and analyzed by immunoblotting.
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6

TNBC Cell Line Culture and Manipulation

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BT549, MDA‐MB‐468 and MDA‐MB‐436 cell lines, which all belong to triple‐negative breast carcinoma cells, were purchased from Cell Bank of the Institute of Basic medicine, Chinese Academy of Medical Sciences (Beijing, China), or obtained as NCI‐ICBP45 kit procured through American Type Culture Collection (ATCC; ATCC Breast Cancer Cell Panel, Manassas, VA, USA). BT549 cells were cultured in RPMI 1640 medium (Boster, Wuhan, China) supplemented with 10% FBS (Gibco, Carlsbad, USA), 1% antibiotics and 0.023 IU·mL−1 bovine insulin (Sigma‐Aldrich, Saint Louis, MO, USA). MDA‐MB‐436 and MDA‐MB‐468 cells were cultured in Dulbecco's modified Eagle's medium (Boster) with 20% or 10% FBS (Gibco) and 1% antibiotics. All cells were kept at 37 °C and 5% CO2. The short hairpin RNA (shRNA) product of SGLT1 (sh‐SGLT1) with a targeted sequence of ATCTTTCTCTTATTGGCAA and its negative control (sh‐NC) were purchased from GeneChem (Shanghai, China) and transfected into cells according to manufacturer’s instructions. Short interfering RNA (siRNA) oligos against SGLT1 (MU‐007589‐01‐0002) were purchased from Dharmacon (Lafayette, CO, USA). Sequences are available from Dharmacon or upon request. As a negative control, we used siGENOME RISC‐Free siRNA (Dharmacon). Cells were transfected with the indicated siRNA oligos at a final concentration of 35 nm using Dharmafect 2 reagent (Dharmacon).
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7

Quantifying Gene Expression in Cell Lines

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NIH3T3 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) with 10% fetal bovine serum (FBS) at 37°C. HMECs and HMLER cells were cultured in HuMEC ready medium (12752010, Life Technologies). Dharmafect 2 reagent (Dharmacon) was used to transfect siRNA at 40 nM. The tetracycline-regulated rat Ubtf1 and Ubtf2 MEF-3T3 cell lines were established as reported in Sanij et al. (2008) (link). Cells were lysed, RNA was extracted, and first-strand cDNA was synthesized using random hexamer primers and Superscript III (Invitrogen). Quantitative PCR (qPCR) was performed in duplicate using the FAST SYBR Green dye on the StepOnePlus real-time PCR system (Applied Biosystems). Primer sequences are listed in (Supplemental Table 20).
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8

Transfection and Silencing Assays

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Validated pools of FBXW7α-, MCL1-, PLK1-siRNA and non-targeting siRNA as negative control were obtained from GE Dharmacon (ON-TARGETplus SMART pools L-004264, L-004501, L-003290, and D-001810). Transfections were carried out using DharmaFECT 2 reagent (GE Dharmacon) according to manufacturer's instructions. All siRNA pools were used at 50 nM. Cells were subjected to different treatments 24 h after silencing. Transient transfections of pCMVHA and pCMVHA-FBXW7 plasmids [28 (link)] were carried out using FuGENE reagent (Promega) according to manufacturer's instructions. Cells were subjected to different treatments 24 h after transfection.
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9

Stable and Transient Knockdown of EP4 and P-selectin

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For stable knockdown of EP4 gene, HEK293T cells were transfected with pLKO.1 lentiviral vector TRCN0000000204 or TRCN0000000205 (Thermo Scientific) encoding shRNAs targeting human EP4. Lentiviral supernatants were collected, and used either separately or in combination to transduce ACHN and SN12C. Lentiviral vector targeting GFP was used to establish control cells. Cells were selected with 2 μg/ml puromycin (Sigma-Aldrich) commencing 48 h after transduction to establish stable lines. Stable knockdown cells were maintained in complete medium containing 1 μg/ml puromycin. For transient knockdown of EP4 or P-selectin gene, 50 nM SMARTpool ON-TARGETplus siRNA (Dharmacon) were transfected into ACHN and SN12C cells with DharmaFECT 2 reagent (Dharmacon). To rescue CD24 expression, EP4 stable knockdown cells were transfected with pCMV6-Entry-CD24 (RC209542, Origene) or control pCMV6-Entry (PS100001, Origene) plasmid. To label cells, wild type ACHN and SN12C were transfected with GFP expressing lentiviral vector pEGIP (Addgene). Stable expressing cells were selected with 2 μg/ml puromycin.
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10

Regulating VEGFR2 in Lung Cancer Cells

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Small interfering RNAs (siRNA) targeting siRNA control (ON TARGETplus control siRNA, 100 nM) and VEGFR2 (ONTARGET plus smartpool, 100 nM) (Dharmacon, Inc., UK) smartpools were transfected into H441 cells using DharmaFECT 2 reagent (4 μl/ml, Dharmacon, Inc.) according to manufacturer's instructions. For the proliferation assay end point, cells were incubated in the transfection media for 24 h. The transfection media was removed and replaced with 100 μl of fresh 0.2% FBS DMEM/F12. DMEM/F12 treated with ± FBS or VEGF was added and plates were incubated for a further 4 days. At this point the cells were stained with crystal violet, allowed to dry and eluted with glacial acetic acid. The absorbance was read at 590 nm using the POLARstar Omega plate reader.
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