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Small interfering rna sirna

Manufactured by GenePharma
Sourced in China

Small interfering RNA (siRNA) is a type of laboratory equipment used in molecular biology research. siRNA is a double-stranded RNA molecule that can effectively silence the expression of specific genes by binding to and degrading their corresponding messenger RNA (mRNA) molecules. This process is known as RNA interference (RNAi) and is a valuable tool for studying gene function and regulation.

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27 protocols using small interfering rna sirna

1

Ovarian Cancer Cell Line Transfection Protocol

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Ovarian cancer cell lines SKOV3 and OVCAR3 were obtained from Guangzhou Jennio Biotech Co.,Ltd.
(Guangzhou, Guangdong, China) and cultured in RPMI1640 medium (Sigma, St. Louis, MO, USA) supplemented with 10% fetal bovine serum (FBS) (Sigma), 100 U/ml penicillin and 100 µg/ml streptomycin (HyClone, Logan, UT, USA) at 37 °C, 5%CO 2 . Cells were seeded in 12-well plates (5 × 10 4 per well) and transfected with miR-15a-5p mimic or the negative control (miR-NC) (GenePharma, Shanghai, China). The pcDNA3.1-PELP1 expression plasmid was constructed by GenePharma (Shanghai, China).
Small interfering RNA (siRNA) was used for the knockdown of PELP1. Pooled PELP1-speci c siRNAs were purchased from Santa Cruz Biotechnology (Santa Cruz, CA, USA). Lipofectamine™ 3000 was used for transfection according to the manufacture's instruction.
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2

Regulation of β-catenin Signaling in Cells

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The following reagents were used in the present study: Fetal bovine serum (FBS), RPMI-1640 (Hyclone; GE Healthcare Life Sciences, Logan, UT, USA), lithium chloride (LiCl; Sigma-Aldrich, St. Louis, MO, USA), CellTiter 96 AQueous One Solution Cell Proliferation Assay (MTS assay; Promega Corporation, Madison, WI, USA) and FITC Annexin V (BD Biosciences, San Jose, CA, USA). Rabbit polyclonal anti-β-catenin (cat. no. sc-7199; 1:2,000 dilution; Santa Cruz Biotechnology, Inc., Dallas, TX, USA), mouse monoclonal anti-β-actin (cat. no. sc-130065; Santa Cruz Biotechnology, Inc.; 1:1,000 dilution), rabbit monoclonal anti-phosphorylated (p)-β-catenin (cat. no. 4176; 1:1,000 dilution; Cell Signaling Technology, Inc., Boston, MA, USA), rabbit monoclonal anti-Bcl-xl (cat. no. 2764; Cell Signaling Technology, Inc.; 1:1,000 dilution), horseradish peroxidase (HRP)-conjugated polyclonal goat anti-mouse IgG (cat. no. SA0001-1; 1:5,000 dilution; ProteinTech Group, Inc., Chicago, IL, USA) and goat anti-rabbit IgG (cat. no. SA0001-2; 1:5,000 dilution; ProteinTech Group, Inc.) antibodies were used for western blotting. Small interfering RNA (siRNA; Shanghai GenePharma Co., Shanghai, China) and Lipofectamine 2000 transfection reagent (Invitrogen; Thermo Fisher Scientific, Inc., Waltham, MA, USA) were also used.
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3

Overexpression and Silencing of THAP11 and c-Myc

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THAP11 and c-Myc overexpression plasmids, pGV141-THAP11 and pGV141- c-Myc, and the negative control plasmids, pGV141, were purchased from GENECHEM (Shanghai, China). Small interfering RNA (siRNA) targeting THAP11 (si-THAP11) and control siRNA were from Gene-Pharma (Shanghai, China). The siRNA sequences were shown in Table 1. MKN-45 cells were cultured until the cell confluence reached 60-80%, and the corresponding overexpression plasmids or RNA interference fragments was transfected with lipofectamine 2000 (Thermo Fisher Scientific) according to the manufacturer's instructions.
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4

Glioma Cell Culture and Transfection

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The human glioma cell lines (U87, U251, SHG44, A172) were purchased from the American Type Culture Collection (ATCC, Manassas, VA) as well as normal human astrocytes (NHA). Cell were cultured with RPMI‐1640 medium (Gibco, Carlsbad, CA), supplemented with 10% foetal bovine serum (FBS, Gibco, Carlsbad, CA) and 100 U/mL penicillin/streptomycin (Life Technologies, CA) in humidified incubator with 5% CO2 at 37°C. Small interfering RNA (siRNA) was synthesized by GenePharma Company (Shanghai, China). The transfection of siRNA (si‐LINC00511 and negative controls) was separately transfected into glioma cells using Lipofectamine 2000 reagent (Invitrogen, Carlsbad, CA). All the sequences were showed in the Table S1.
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5

Generating Stable Knockout Cell Lines

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Human HCT-116 and SW480 CC cell lines (American Type Culture Collection, Manassas, VA, USA) were cultured in Dulbecco’s modified Eagle’s medium containing 10% fetal bovine serum (FBS; both from Thermo Fisher Scientific Inc., Waltham, MA, USA) with 1% streptomycin and penicillin, at 37°C under a humidified 5% CO2 atmosphere.
Cells were transiently transfected using Lipofectamine 2000 (Invitrogen) as described by the manufacturer. Small interfering RNA (siRNA) was purchased from GenePharma (Shanghai, China) The sense and anti-sense si-U62317.4 sequences were: 5′-GAAGAGAAGGACAAGUUGACG-3′ and 5′-UCAACUUGUCCUUCUCUUCUG-3′, respectively. We created a stable knockout U62317.4 cell line using short hairpin RNA (shRNA) targeting U62317.4 (sh-U62317.4; General Biosystems, Anhui, China) with the sense and anti-sense sequences, 5′-GATACTTGATCCTGATAAA-3′ and 5′- TTTATCAGGATCAAGTATC-3′, respectively.
Lentiviral particles were obtained as described (16 (link)). HCT-116 cells were directly infected with Polybrene (Santa Cruz Biotechnology, Dallas, TX, USA) for 24 h and then, transfected cells were screened for 7–10 days with 2 μg/mL of puromycin (Invitrogen).
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6

Transfection of METTL3 siRNA in Cell Lines

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Lipofectamine® 2000 reagent (Invitrogen; Thermo Fisher Scientific, Inc.) was used for cell transfection, according to the manufacturer's protocol. TE-9 and Eca-109 cells (5x105 cells/ml) in the logarithmic growth phase were transfected with 100 nM negative control (NC) small interfering RNA (siRNA) or 100 nM METTL3-specific siRNAs (Shanghai GenePharma Co., Ltd.) at 37˚C. Following transfection for 48 h, METTL3 expression levels were evaluated using reverse transcription-quantitative PCR (RT-qPCR).
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7

Isoproterenol-Induced Cardiac Fibrosis Model

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Isoproterenol (ISO) was supplied by Tokyo Chemical Industry Co., Ltd. (Japan). Drugs BEL and Trimetazidine (TMZ) used in the study were obtained from Chengdu Alfa Biotechnology (China) and Nanjing Zenkom Pharmaceutical Co., Ltd. (China), respectively. The staining kits for hematoxylin-eosin (HE) and Masson trichrome were provided by Servicebio Technology Co., Ltd. (China). Collagen I (cat. no.AF7001) and Collagen III (cat. no.AF0136) antibodies were offered by Affinity Biosciences (USA). Primary antibodies for α-SMA (cat. no. ab32575), SOX9 (cat. no. ab185966), Smad3 (cat. no. ab40854), phospho-Smad3 (S423 + S425) (cat. no. ab52903), and TGF-β1 (cat. no. ab92486) were supplied by Abcam Technology (United Kingdom). Glyceraldehyde 3-phosphate dehydrogenase (GAPDH, cat. no. 60004-1-Ig) was obtained from Wuhan Proteintech Biotechnology (China). HRP-conjugated antirabbit and antimouse IgG (cat. nos.ZdR-5306 and ZdR-5307) antibodies were offered by Beijing ZSGB Bioengineering Institute (China). DMEM medium was gained from Gibco (USA). The fetal bovine serum (FBS) and penicillin/streptomycin were provided by Biological Industries (Israel). Small interfering RNA (siRNA) was obtained from Shanghai GenePharma (China). Recombinant human TGF-β1 and LipofectamineTM 3000 reagents were supplied by Thermo Fisher Scientific (USA).
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8

Cloning and Regulation of c-Cbl, IL10, and IL6

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All primary antibodies used in this study including for immunoblot, immunoprecipitation, and ChIP, and second antibodies are listed in table S1. All vectors used in this study are listed in table S2. The mouse gene of c-Cbl was amplified by PCR using full-length cDNA from mouse BMDCs as a template. The PCR products of c-Cbl were inserted into the vector pcDNA6. The promoter of il10 and il6 was amplified by PCR from mouse genomic DNA and then cloned into the PGL3 enhancer vector. The PCR primers for cloning of c-Cbl and the promoter region of il10 and il6 are listed in table S3. His-Ub plasmid was described and provided by P. Wang (Tongji University School of Medicine, Shanghai, China) (50 (link)). Hemagglutinin (HA)-RelB, Flag-RelB, and Flag-p65 were described in our previous study (33 (link)).
LPS (L5024), curdlan (C7821), Pam3Cys-Ser-(Lys)4 (Pam3CSK4, 506350), and α-mannans (M7054) were purchased from Sigma-Aldrich, and recombinant murine granulocyte-macrophage colony-stimulating factor (GM-CSF) and M-CSF were purchased from PeproTech. Small interfering RNA (siRNA) targeting the gene of RelB and c-Abl and the nontargeting control siRNA (NC) were synthesized from GenePharma (Shanghai).
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9

NSCLC Cell Line Transfection Protocols

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The Academy of Military Medical Sciences (Beijing, China) provided the human NSCLC cell line A549 and H1299. In a 5% CO2 humidified incubator at 37°C and RPMI 1640 medium (Thermo Scientific, USA) supplemented with 10% fetal calf serum (FCS) (Thermo Scientific), these cells were cultured. For transfections, pcDNA3.1(+)-MRUL and pcDNA3.1(+) vector (DingGuoChangSheng Biotechnology Co. Ltd., Beijing, China), 50 to 100 nM small interfering RNA (siRNA) (Gene Pharma Co., Shanghai, China), Lipofectamine 2000 (Invitrogen Int., USA), and lentivirus vector-MRUL(−) (RiboBio Co., Guangzhou, China) were employed following the manufacturer's recommendations as portrayed earlier (19). siRNA sequences are presented here: siRNA targeting NR_024549 (MRUL), siMRUL-1, GGCCUUUGUUUGCAGUUUATT; siMRUL-2, AACACUUUCCUGUUUUGGGUC; siMRUL-3, AGUUUCUACUGUUACUGUGUC; siP-gp (targeting P-gp), GGGACAGGAAUAAUUAUAUTT; and siNC (negative control), UUCUCCGAACGUGUCACGUTT.
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10

Analyzing Autophagy in HK-2 Cells

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The human proximal tubular epithelial cell line HK-2 was obtained from the American Type Culture Collection (ATCC), ATCC Cat# CRL-2190, RRID:CVCL_0302. The sources of the antibodies used in this study were as follow: anti-LC3B (Cell Signaling Technology, 2775), anti-LC3B (Novus, NB100-2220), anti-SQSTM1 (Abcam, ab109012), anti-Cleaved Caspase 3 (Sigma-Aldrich, AB3623), anti-GAPDH (Cell Signaling Technology, 2118), anti-PINK1 (Novus, BC100-494), anti-PARK2/Parkin (Cell Signaling Technology, 4211), anti-Tom20 (Santa Cruz Biotechnology, sc-17764), HRP-labeled Goat Anti-Rabbit IgG (Beyotime, A0208), HRP-labeled Goat Anti-mouse IgG (Beyotime, A0216), Alexa Fluor 488 (Thermo Fisher Scientific, A-21222). Human serum albumin (HAS/ALB) was purchased from Sigma Aldrich (St. Louis, MO, USA). Small interfering RNA (siRNA) targeting human Parkin, negative control siRNA, Parkin plasmids, and control empty plasmid vector were purchased from GenePharma (Shanghai, China). The sequences of siRNA oligonucleotides were sa follows: Parkin siRNA, 5 ′ -CCUUCUGCCGGGAAUGUAATT; control siRNA, 5 ′ -UUCUCCGAACGUGUCACGUTT.
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