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ShRNA (short hairpin RNA) is a type of laboratory equipment used in molecular biology research. It functions as a tool for gene silencing, allowing researchers to investigate the role of specific genes in cellular processes. ShRNA is designed to trigger the degradation of target mRNA molecules, effectively reducing the expression of the corresponding genes. The core function of ShRNA is to provide a means for targeted gene knockdown in experimental settings.

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52 protocols using shrna

1

Targeting CCR4 in Hepatocellular Carcinoma

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Green fluorescent protein (GFP)-labeled lentiviral vector and four short hairpin RNA (shRNA) targeting CCR4 were purchased from Genepharma Shanghai. We transfected Lentivirus particles were into the HCC cells according to the manufacturer’s instruction. 4 targeted CCR4 sequences were listed as follows: shRNA1: 5′-GGT TCT GGA CAC ACA CTT ACA-3′; shRNA2: 5′-GCA CCT TTG AAA ACT GAT TGG-3′; shRNA3: 5′-GGG AGA TTC GCA AAT AGT ACA-3′; shRNA4: 5′-GCA CAC CAT GGA GTC TGG ATC ATG A-3′. Lipofectamine 2000 (Invitrogen Corporation) was used to mediate shRNA and then transfected into cells. G418 were used to select the stable transfected cells. And plasmid shRNA2 proved to have strongest efficiency and we used this for further research.
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2

Knockdown of lncRNA AK139328 in PC12 cells

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Knockdown of AK139328 expression was performed using short hairpin RNA (shRNA) targeting AK139328 (shRNA-AK139328-1; 5′-CACCGGAAACTCAGCTATCACATGCCGAAGCATGTGATAGCTGAGTTTCC-3′), shRNA-AK139328-2 (5′-CACCGCAGCAGAAAGACATGTTTGGCGAACCAAACATGTCTTTCTGCTGC-3′) and corresponding scrambled negative control (shRNA; 5′-CACCTTCTCCGAACGTGTCACGTTTCAAGAGAACGTGACACGTTCGGAGAATTTTTTG-3′), which were both synthesized by Shanghai GenePharma Co., Ltd. PC12 cells were transfected with 500 ng/µl shRNA-AK139328-1/2 or shRNA using Lipofectamine® 2000 reagent (Invitrogen; Thermo Fisher Scientific, Inc.), according to the manufacturer's protocol. The cells were harvested for use in subsequent experiments at 48 h post-transfection.
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3

GSTO1 Manipulation in NSCLC Cells

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Cell transfections were performed using Lipofectamine® 2000 reagent (Invitrogen; Thermo Fisher Scientific, Inc.), according to the manufacturer's protocol. Untransfected cells were used as a blank control. Briefly, 4×105 H2122 or A549 cells were plated into a six-well plate and cultured to 90–95% confluence. The overexpression of GSTO1 in NSCLC cells was induced through transfection with a pcDNA3.1 plasmid (4 µg; Invitrogen; Thermo Fisher Scientific, Inc.) carrying the GSTO1 cDNA insert, with an empty vector (4 µg) as the negative control (pcDNA3.1-NC). The knockdown of GSTO1 in NSCLC cells was induced using 2 µg short hairpin RNA (shRNA; Thermo Fisher Scientific, Inc.) against GSTO1, using stable non-specific shRNA (2 µg) as the NC (shRNA-NC). The shRNA-NC sequence was 5′-CCGGCCTAAGGTTAAGTCGCCCTCGCTCGAGCGAGGGCGACTTAACCTTAGGTTTTTC-3′ and the shRNA-GSTO1 sequence was 5′-GCTGGAAGCAATGAAGTTA-3′. Cells were transfected for 24 h at 37°C in an atmosphere containing 5% CO2 to obtain stably transfected cells for future use. At 48 h post-transfection, the overexpression and knockdown of GSTO1 was confirmed using reverse transcription-quantitative PCR (RT-qPCR) and western blotting.
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4

CHIP and TRAF2 Gene Knockdown

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The short hairpin RNA (shRNA) specifically targeting the human CHIP gene or the human TRAF2 gene was designed and synthesized from Invitrogen (Beijing, China). The sequences of CHIP-shRNA are 1013–1032: 5′-AGGCCAAGCACGACAAGTAC-3′. The sequences of TRAF2-shRNA are 1224–1242: 5′-GATGTGTCTGCGTATCTAC-3′. Either the shRNA-CHIP or the shRNA-TRAF2 was subcloned into the pSilencer3.1-H1-neo plasmid (Cat Nr. 5770, Thermo Scientific™, China), which was linearized by restriction endonucleases HindIII and BamHI. Cells were pre-cultured to 60–80% confluence and transfected using Lipofectamine 2000 (Cat Nr. 12566014, Thermo Scientific™, China) for 6 h according to manufacturer’s protocol. To obtain stably transfected clones, cells were selected in the media containing G418 (400 ng/µl, Cat Nr. E859-5G, Amresco, USA) for 2 weeks.
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5

Lentiviral Knockdown of IGF1R

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Vectors (GIPZ) encoding the following microRNA-adapted short hairpin RNAs (shRNA) 5’-TGACTGTGAAATCTTCGGC-3’ (mouse/human IGF1R), 5’- TTAGTTCCATGATGACCAG-3’ (mouse IGF1R) packed in high-titer lentiviral particles were purchased from Open Biosystems (Huntsville, AL, USA). These vectors or a vector containing a scrambled shRNA sequence (control shRNA; Open Biosystems) were infected in the presence of 8 μg/ml polybrene (Sigma-Aldrich, Rehovot, Israel) into Mvt-1 or MCF7 cells, all three vectors contained a green fluorescent protein (GFP) marker and puromycin resistance gene. Stable knockdown of the IGF1R was achieved by selection with 2 μg/ml puromycin (Sigma-Aldrich).
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6

Knockdown of WWP2 and WWP1 in Cells

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Vectors containing a control short hairpin RNA (shRNA) and WWP2 shRNA (shRNA1, 5′-CAGGAUGGGAGAUGAAAUAUU-3′; shRNA2, 5′-ACAUGGAGAUACUGGGCAAUU-3′), WWP1 shRNA (shRNA1, 5′-ATTGCTTATGAACGCGGCT-3′; shRNA 2, ACAACACACCTTCATCTCC-3′) were purchased from Open Biosystems and were transfected into cells with Lipofectamine using standard protocols. WWP2 siRNA described earlier (23 (link)) and prevalidated siRNAs for PPM1G (catalog numbers S102658684 and S102658691) were purchased from Qiagen and transfected using Oligofectamine using standard protocols.
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7

Lentiviral Knockdown and Overexpression

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Lentivirus-mediated p38 MAPK knockdown or Runx2 overexpression was performed as previously described [5] (link), [6] (link). Lentiviral vector encoding a 21-nucleotide p38 MAPK short hairpin RNA (shRNA) was purchased from Open Biosystems and packaged into lentiviral particles. Lentiviral construct expressing wild type Runx2 was generated as we previous described [33] (link). Viral transductions were performed by incubating VSMC with recombinant lentiviruses in growth media supplemented with 10 µg/mL Polybrene (Sigma). After 24 h, cells were washed with PBS and kept in growth media containing puromycin for 2 weeks to select stable transfectants.
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8

Stable CDCP1 Knockdown in CRC13 Spheroids

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CDCP1 expression was stably reduced in cells grown as spheroids isolated from a previously generated patient-derived xenograft (PDX), designated CRC13, as previously described [27 (link), 28 (link)]. Cells from CRC13 spheroids mechanically dissociated in phosphate-buffered saline (PBS) containing EDTA (0.48 mM) were stably infected with a pLKO.1 lentiviral CDCP1 targeting shRNA (target sequence: GCTCATAAGAGCATCGGTTTA; Open Biosystems, Millennium Science, Surrey Hills, Australia), or as a control, a nontargeting (control) shRNA (Addgene, Watertown, MA, USA) construct. Stably infected cells were grown as spheroids and selected in media containing puromycin (2 µg/ml) generating cells designated CRC13-shScr and CRC13-shCDCP1 which were propagated as subcutaneous tumors in mice as described below.
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9

Efficient siRNA Transfection and shRNA Lentiviral Delivery

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For siRNA transfection cells were plated at a density of 50–80% on 6-cm dishes 1 d before transfection. siRNAs were purchased from Dharmacon and were used at a final concentration of 20 nM. Transfection was carried out using the Lipofectamine RNAiMAX reagent (Invitrogen) according to the manufacturer’s instructions. Lentiviral vector plasmids for stable, constitutive or inducible expression of secreted luciferases GLuc and CLuc coupled to p53 or nontargeting control shRNAs were described previously29 (link). shRNA sequences from Open Biosystems are as follows: shFancD2.2 (V2LHS_139155), shFancD2.3 (V3LHS_383034), shFancD2.4 (V3LHS_383035). siRNA sequences: siFancD2.6 CAACATACCTCGACTCATT, siFancD2.8 GGAGATTGATGGT CTACTA, simTOR.8 GGCCAUAGCUAGCCUCAUA, simTOR.9 CAAAGGA CUUCGCCCAUAA, simTOR.10:GCAGAAUUGUCAAGGGAUA, simTOR.11 CCAAAGCACUACACUACAA.
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10

Analyzing Notch-mediated Smad Activation

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Activation/phosphorylation of Smad3 (p-Smad3) in lung fibroblasts was detected using antibodies from Cell Signaling (Cat. No. 9520). Notch 1 (Clone TRCN0000025902) and 3 (clone TRCN0000075570) were silenced with shRNA (Open Biosystems) in lung fibroblasts to test the contribution of each of these Notch receptors on Notch-mediated activation in lung fibroblasts. An electrophoretic mobility shift assay (EMSA) kit (Panomics, Fremont, CA) was used to detect Smad protein DNA binding activity in lung fibroblasts. 10 μg nuclear extract was mixed with a labeled Smad 3/4 binding element probe (Panomics, Fremont, CA, Cat. No. AY1042P) and analyzed. Attenuation of Smad activation was assessed by comparing the optical density of shifted bands among groups.
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