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26 protocols using sictrl

1

Plasmid and siRNA Transfection Assay

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pcDNA3.1/XPC-V5-His plasmid containing XPC cDNA was described previously [47 (link)]. XPC shRNA (short hairpin RNA) were purchased from Sigma (TRCN0000083118, TRCN0000083119). XPC siRNA and a scramble non-targeting siRNA (siCtrl) were purchased from Dharmacon (siGENOME human XPC siRNA SMARTpool, siXPC-#1: 5′-GCA AAU GGC UUC UAU CGA A-3′, siXPC-#2: 5′-GGA GGG CGA UGA AAC CUU U-3′, siCtrl: 5′-UUC UCC GAA CGU GUC ACG U-3′). pcDNA3/E-Cadherin plasmid containing E-Cadherin cDNA (NM_004360.3) was purchased from Addgene (Addgene plasmid #45769, ref: [49 (link)]) The plasmids and siRNA were transfected into cells by using Lipofectamine 2000 reagents (Life Technologies) according to manufacturer's instructions.
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2

TRIM25 and Caspase-2 Knockdown Assay

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Subconfluent cells were transiently transfected with siRNAs by employing the Oligofectamine reagent from Invitrogen (Karlsruhe, Germany) according to the manufacturer′s instructions.
The transient knockdown of genes was achieved by transfection of siRNA-duplexes from 50 nM validated siRNAs from Thermo Scientific against human TRIM25 (ID#15204, “siTRIM25#1”), or alternatively, a mixture of FlexiTube siRNAs for human TRIM25 (SI0000072170, SI0000072163, SI0000072156, and SI0000072149, “siTRIM25#2”) from Qiagen (Hilden, Germany) or the same amounts of FlexiTube siRNA-duplexes for caspase-2 (SI00299551, “siCasp-2”) from Qiagen (Hilden, Germany). For double siRNA transfections with siTRIM25#1 and siCasp-2, each siRNA was employed at a concentration of 25 nM while a non-targeting siRNA (siCtrl, #D001206-13) from Dharmacon (St. Leon-Rot, Germany) was used as a control.
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3

Hypoxia-mediated ATF4 knockdown

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Cells were transfected with ON-TARGETplus SMARTpool siRNA against murine ATF4 (siATF4) or nontargeting control (siCtrl, Dharmacon, Lafayette, CO) using polyethylenimine (Polysciences, Warrington, PA) in serum-free media. After 12 h, transfection media was replaced with fresh serum-containing media, and cells were grown for an additional 48 h in hypoxia or normoxia prior to analysis.
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4

Regulation of Exponential Cell Growth

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Exponentially growing PCCs were transfected using Dharmafect®1 Reagent (T-2001–01, Dharmacon) and with control (CN-001000–01) or miR-29a mimic (C-300504–07), or the following siRNAs from Dharmacon: siCTRL (D-001810–10-05), siMYC (L-003282–02-0005), siSMAD4 (L-003902–00-0005), siGLI3 (L-011043–00-0005), siMYBL2 (L-010444–00-0005), siLOXL2 (L-008020–01-0005), siCLDN1 (L-017369–00-0005), siHGK (L-003971–00-0002), and siNRAS (L-003919–00-0005), from Qiagen: miRNA inhibitor control (339126) or LNA miR-29a inhibitor (339121), following manufacturer’s protocol. Total protein or RNA was isolated 48 hrs post-transfection for western blot or qPCR analyses.
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5

Silencing of TF and DPP4 in hVSMCs

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For TF silencing, hVSMCs were transfected with siCtrl or siRELA, siEGFR, siSP1, or siFOS (25 nM) (Dharmacon); 72 hours later, senescence was induced with Doxo for an additional 72 hours. For DPP4 silencing, hVSMCs were transfected with siCtrl or siDPP4 (25 nM). For siRNA screening, a custom siRNA library plate was designed including siRNA pools to silence CFD, C9, CFB, C4A, C7, FGB, FGG, FX, FV, FII, SERPINE1, TIMP1, MMP1, and PLAT. This included a nontargeting control siRNA. Sequences and catalog numbers for siRNA custom screening are available in Supplemental Table 1. All small RNA transfections were performed using Lipofectamine RNAiMAX (Thermo Fisher Scientific).
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6

Knockdown of GRP78, HRAS, NRAS, and KRAS

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The cells were seeded in triplicate on 6cm dishes at approximately 60-70% confluency and allowed to attached overnight. Next day, the cells were transfected with siRNAs targeting GRP78 (si78) or scrambled control (siCtrl) using the Lipofectamine RNAiMAX Transfection Reagent (ThermoFisher Scientific, Waltham, MA, Cat# 13778075) in accordance with manufacturer's recommendation for forward transfection. For reverse transfection, the cells were mixed with the transfection mix at the same time as seeding and the cells were incubated with the siRNA transfection mix for 48 hr before harvesting for analysis. The custom siRNAs for siCtrl, siGRP78, and siKRAS were purchased from GE Healthcare Dharmacon, Inc. (Chicago, IL) with the following sequences: siCtrl 5’- GAGAUCGUAUAGCAACGGU -3’, si78 5’- GGAGCGCAUUGAUACUAGA-3’ and siKRAS (ON-TARGETplus siRNA Cat# J-005069-08-0002). The custom siRNAs for HRAS and NRAS were purchased from Integrated DNA Technologies (IDT, Coralville, IA) with the following sequences: siHRAS 5’-UAAUUUACUGUGAUCCCAUCUG-3’, siNRAS 5’-UUCAGUUUCAUCUUUCUCCUGG-3’.
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7

HDAC9 Knockdown and Overexpression in HASMCs

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siRNA directed against HDAC9 (siHDAC9) and scrambled control siRNA (siCTRL) were obtained from Dharmacon (SMARTpool, Thermo Scientific). HASMCs were transfected with siRNA using Lipofectamine RNAiMAX reagent, as described by the manufacturer (Life Technologies).
Recombinant adenoviruses expressing either human wild-type HDAC9 (NM_058176) with a C-terminal Enhanced Green Fluorescent Protein (eGFP) tag or expressing eGFP alone were obtained from Vector Biolabs (human adenovirus type 5 [dE1/E3], promoter: cytomegalovirus, Catalog #1768, Malvern, PA). HASMCs were transduced with the adenovirus vectors in regular growth medium. After 24 hours, cells expressing eGFP were detected using fluorescent microscopy. RNA and protein levels were analyzed by qPCR and Western blot, respectively, 8 days after transduction.
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8

siRNA-Mediated Knockdown of IFITM Proteins

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Pre-designed pooled siRNAs targeting IFITM1 (si-IFITM1), IFITM2 (si-IFITM2), and IFITM3 (si-IFITM3), as well as negative control scramble siRNA (si-Ctrl) were purchased from Dharmacon (Lafayett, CO, USA). Cells were transfected with different siRNAs using Lipofectamine 2000 reagent (Thermo Fisher Scientific).
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9

Knockdown of TRIM25 and hnRNPH in Epithelial Cells

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The epithelial cells were plated on 6 cm dishes to obtain 30–40% confluency at the day of transfection. The subconfluent cells were transfected with siRNAs by using the Oligofectamine reagent (Invitrogen) by following the manufacturer’s instructions. Gene silencing was performed by the transfecting of siRNA duplexes from 50 nM of validated siRNAs against human TRIM25 (ID#15204, “siTRIM25#1”) from ThermoFisher Scientific or, alternatively, a mixture of FlexiTube siRNAs for human TRIM25 (SI0000072170, SI0000072163, SI0000072156 and SI0000072149, “siTRIM25#2”) from Qiagen (Hilden, Germany). Alternatively, the cells were transfected with the same amounts of FlexiTube siRNA duplexes for hnRNPH (“sihnRNPH#1”) from Dharmacon (St. Leon-Rot, Germany) or from Santa Cruz (“sihnRNP#2”). A non-targeting control siRNA (siCtrl, #D001206-13) was from Dharmacon. The specific silencing of the targeted genes was validated by Western blot analysis.
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10

RNAi Molecules for STAT3 Silencing

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HPLC-purified siRNA and DsiRNA RNAi with indicated (UU) overhangs were obtained from GE Dharmacon: (1) siCTRL sense: 5′-CGU UAA UCG CGU AUA AUA C(UU)-3′, antisense: 5′-GUA UUA UAC GCG AUU AAC G(UU)-3′; (2) DsiCTRL sense: 5′-CGU UAA UCG GCU AUA AUA CGC GUA U-3′, antisense: 5′-AUA CGC GUA UUA UAC GCG AUU AAC G(UU)-3′; (3) siSTAT3 sense: 5′-GGU CAA AUU UCC UGA GUU G(UU)-3′, antisense: 5′-CAA CUC AGG AAA UUU GAC C(UU)-3′; (4) DsiSTAT3 sense: 5′-GGU CAA AUU UCC UGA GUU GAA UUA U-3′, antisense: 5′-AUA AUU CAA CUC AGG AAA UUU GAC C(UU)-3′; (5)Chol-siCTRL: siCTRL with 3′-cholesterol conjugated to the sense strand; (6)Chol-siSTAT3: siSTAT3 with 3′-cholesterol conjugated to the sense strand; (7) Chol-DsiCTRL: DsiSTAT3 with 3′-cholesterol conjugated to the sense strand; (8) Chol-DsiSTAT3: DsiSTAT3 with 3′-cholesterol conjugated to the sense strand. For in vitro studies, lyophilized RNAi molecules were resuspended in sterile, nuclease-free ddH20 [100 μM] as directed (GE Dharmacon) and stored in aliquots [10 μL] at −80°C. For in vivo studies, lyophilized RNAi molecules were resuspended in the indicated buffer on the day of injection.
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