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45 protocols using pepmute sirna transfection reagent

1

Transient Transfection Assay for CXCR4 Knockdown

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The transient transfection assay was carried out in 6-well plates using PepMute™ siRNA Transfection Reagent (SignaGen® Laboratories, USA) according to the manufacturer's instruction. First, PepMute™ transfection buffer was diluted before use, and then 3.3 μl siRNA in 1 ml RPMI 1640 medium was added gently and incubated for 15 min at room temperature. The complexes were added to each well and mixed gently by rocking the plates back and forth. The plates were then incubated at 37°C in a CO2 incubator. After 48 h, cells were collected for further experiments. The CXCR4 siRNA product was purchased from Santa Cruz Biotechnology, Inc. (Santa Cruz, CA).
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2

Modulating Podocyte Cdk5 and p35 Pathways

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Cdk5 siRNA (sc-29263), p35 siRNA (sc-36154), and control siRNA (sc-37007) were ordered from Santa Cruz Inc and delivered to podocytes using Pepmute siRNA transfection reagent (SignaGen Laboratories), according to the manufacturer's instructions. Briefly, podocytes were seeded in a 6-well plate and cultured for 7 days at about 50–60% confluence. For transfection, 5μl siRNA were diluted in 100μl of 1x siRNA transfection buffer (SignaGen Laboratories) in a final concentration of 50 nM siRNA. Three ul of Pepmute reagent were then mixed by pipetting up and down, incubated 15 minutes at RT, and dropped onto the cultured cells. After 72 h, cells were harvested or fixed for further experiments.
Adenovirus-p35 and empty vector (EV) were made and infected according to the methods of previous study [2 (link), 18 (link)].
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3

Knockdown and Overexpression of c-Myc

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For gene knockdown experiments, c-Myc siRNA and non-targeting scrambled siRNA (NS) obtained from Santa Cruz Biotech were transfected into RPMI 8226 cells using PepMute™ siRNA transfection reagent (SignaGen Laboratories). For gene overexpression experiments, cells were transfected with pcDNA3.1-c-Myc, Flag-SUMO1 or HA-Ubiquitin plasmids (Addgene) using GenJet™ in vitro DNA transfection reagent (SignaGen Laboratories).
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4

siRNA Knockdown Optimization Protocol

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The small interfering RNAs (siRNA) used were ON-TARGET plus SMART pool and 4 individual siRNAs for each targeted molecule obtained from Dharmacon (Chicago, IL). As a control, scramble siRNA was also purchased. Transfection was performed with PepMute™ siRNA Transfection Reagent from SignaGen Laboratories (Gaithersburg, MD) using a reverse transfection procedure as recommended by the manufacturer.
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5

SIRT1 Gene Silencing in Degenerative NP Cells

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Double-stranded small interfering RNA (siRNA) for human SIRT1 gene silencing was designed and synthesized by Invitrogen (Invitrogen, USA) to suppress the expression of endogenous SIRT1 of degenerative human NP cells. Sequences of the SIRT1-siRNA were as follows: sense 5′-CCAAGCAGCUAAGAGUAAUTT-3′, antisense 5′- AUUACUCUUAGCUGCUUGGTT-3′. Cells were seeded in 6 wells plate for 24 h and were transfected with SIRT1 or negative control siRNA duplexes using PepMute siRNA Transfection Reagent (SignaGen, SL100566) according to the manufacturer's instructions. After further various treatments, cells were harvested for flow cytometry, and protein extracts were used for Western blot experiments.
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6

siRNA Knockdown of BLK Gene

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The siRNA duplexes targeting BLK were chemically synthesized by GenePharma. The siRNA duplexes were transfected into cells with PepMute siRNA transfection reagent (SignaGen Laboratories) according to the manufacturer’s instructions. The following sequences of human BLK mRNA were targeted:
BLK-RNAi #1: AAGCGACTGTCATCAAGTA,
BLK-RNAi #2: AGGTGGTTCTTTAGATCAC,
Negative control (NC): TTCTCCGAACGTGTCACGT.
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7

Silencing DDIT3 gene expression

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ON‐TARGETplus SMARTPool siRNA targeting human DDIT3 (#L‐004819‐00‐0005) and a scrambled control siRNA (#D‐001810‐10‐05) were purchased from Horizon Discovery. Cells were seeded and siRNA was transfected using PepMute siRNA Transfection Reagent (SignaGen Laboratories, # SL100566) according to manufacturer's protocol. After 24–48h post‐transfection, cells were detached with trypsin and used for downstream experiments.
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8

Knockdown of Smad2 and Smad3 in MDA-MB-231 Cells

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200,000 MDA-MB-231 cells were seeded in T-75 culture flasks for 24 h before being transfected with 25 nM Smad2 or Smad3 siRNA (Santa Cruz Biotechnology) for 4 h in 0.3% PepMute siRNA Transfection Reagent (SignaGen Laboratories, Rockville, MD, USA). Afterwards, a media change was made, and transfected cells were re-suspended and plated on glass slides pre-coated with 145 µg/mL Rat Tail collagen I (Life Technologies Inc., ON, Canada). Cells were left to grow for 24 h before being used in cell culture, flow, and PCR experiments as previously described. The methodologies for optimizing siRNA transfections, control and transfection efficiency experiments are described in Supplemental Methods.
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9

Visualizing Endothelial Cell Signaling

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Histamine dihydrochloride (histamine), PP2, simvastatin, (R)-mevalonic acid lithium salt (mevalonic acid) and imaging buffer components were purchased from Sigma-Aldrich (St. Louis, MO, USA). Vascular endothelial growth factor (VEGF) was obtained from R&D Systems (Minneapolis, MN, USA). NSC23766 and LB42708 were from APExBio Inc (Houston, TX, USA). Lipofectamine™ 3000 Transfection Reagent (LF3000) were purchased from Thermo Fisher Scientific (Waltham, MA, USA). GKT137831 was obtained from Cayman Chemical (Ann Arbor, MI, USA) and PepMute™ siRNA Transfection Reagent was from SignaGen (Frederick, MD, USA).
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10

Lamin A/C Knockdown and Knockout

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Lamin A/C siRNA (Santa Cruz) was introduced into cells using Pepmute siRNA transfection reagent (Signagen) per the manufacturer’s guidelines. Lamin A/C-specific TRIPZ lentiviral shRNA was obtained from Horizon (RHS5087-EG4000). Transduced cells were puromycin selected (5 µg/mL), and induced with doxycycline (1 µg/mL). For gene editing, plasmid pX330-U6-Chimeric_BB-CBh-hSpCas9 (gift from F. Zhang; Addgene plasmid # 42230; http://n2t.net/addgene:42230; RRID: Addgene_42230). We modified the plasmid by introducing a copy of a CMV promoter-controlled RFP gene into the construct. Two lamin A/C-specific sgRNA: sg1: TCTCAGTGAGAAGCGCACGCTGG and sg2: GGCGAGCTGCATGATCTGCGGGG were cloned into the modified plasmid. Lamin A/C KO cells were selected by RFP flow sorting.
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