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16 protocols using 293t cells

1

Stable LDHA Knockdown via Lentiviral shRNA

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The stable knockdown of LDHA expression was achieved using the lentiviral carrying shRNA process. Lentivirus shLDHAs (shLDHA-1: 5′-GGCAAAGACTATAATGTAA-3′, shLDHA-2: 5′-TAAGGGTCTTTACGGAATA-3′) and a non-specific control shRNA were cloned into the pLVshRNA-EGFP (2A) puro vector. The target plasmids and lentivirus packaging plasmids pGag/Pol, pRev, and pVSV-G were co-transfected with 293T cells according the manufacturer's instructions (GenePharma, China). The virus-containing supernatant was collected, filtered, and infected HSC3, SCC15 cells with 5 μg/ml Polybrene (H8761, solarbio, China). The infected cells were screened with puromycin (HSC3: 3 μg/ml, SCC15: 8 μg/ml) (P8230, solarbio, China) for 15 days.
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2

TLN-1 Gene Silencing in MHCC-97L Cells

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A shRNA sequence targeting the TLN-1 gene (GenBank. No. NM_006289.3) (5’-GCTCGAGATGGCAAGCTTAAA-3’) and one nonspecific sequence 5’-TTCTCCGAACGTGTCACGTTTC-3’ (scramble shRNA) used as the negative control which did not have any homology with the target gene were designed and packaged into Lentivirus and transduced into 293 T cells by Shanghai GenePharma Co., Ltd (China).
For TLN-1 silencing, 0.5 × 105 MHCC-97 L cells were plated in 24-well plates in complete culture medium for 24 h. Then, cells were transduced for 72 h with Lentivirus-mediated TLN-1-shRNA and scramble shRNA, respectively (Shanghai GenePharma Co., Ltd, China), under puromycin selection. Afterwards, the transduced cells were cultured in DMEM containing 10 % FBS and 3 μg/ml of puromycin for 12 days (changing the medium every 3 days), and stably transduced cells were obtained. TLN-1 mRNA and protein levels were assessed by real-time RT-PCR and western blot.
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3

Modulating Autophagy in Cardiac Cell Injury

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BECN1 fragments and mutants were synthesized by Shanghai GenePharma Co., Ltd. as follows: BECN1-siRNA, 5′-GCGGACAATTTGGCACGATCA-3′ and negative control (NC)-siRNA: 5′-TTCTCCGAACGTGTCACGT-3′. The Lentiviral plasmid LV3(H1/GFP&Puro)-BECN1-Rat-1157 was obtained from Shanghai GenePharma Co., Ltd. 293T cells (Shanghai GenePharma Co., Ltd.) were co-transfected with the second-generation lentiviral plasmid (10 µg) and packaging plasmids (pGag/Pol, pRev, PVSV-G), and mixed according to the ratio of 2:1:1:1. Incubated at 37°C in 5% CO2 incubator for 48 h. Lentivirus was produced and H9c2 cells were transduced for 48 h at 37°C with 5 µl/well BECN1-siRNA (1 µg/µl)or NC-siRNA, the titer of BECN1-siRNA was determined to be 3×108 TU/ml, and the MOI for H9c2 infection was 20. After lentiviral transduction and under the same conditions for 48 h. Then, 10,000 U/ml penicillin-streptomycin was used for maintenance, 5 µg/ml puromycin was used to screen cells and protein expression levels of BECN1 were assessed using western blotting. Following stable transfection, H9c2 cells were treated with 50 µmol/l NaHS for 1 h at 37°C, then stimulated with 5 µg/ml LPS for 24 h at 37°C. H9c2 cells were divided into treatment groups as follows: i) LPS; ii) BECN1-siRNA + LPS; iii) LPS + NaHS and iv) BECN1-siRNA + LPS + NaHS.
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4

Lentiviral Knockdown and Overexpression in PC12 Cells

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Lentiviral sh-METTL14, sh-UBR1, sh-YTHDF1, sh-YTHDF2, and/or NCS (GenePharma) were transfected into PC12 cells. The cells were treated with TBHP for 48 h after transfection. The lentiviruses were generated. Specifically, the overexpression (LV-UBR1) or silencing (sh-UBR1: UUGUACAUUCUCUUCUUGCUU; sh-METTL14: AAGUUUCUCUUGUUUCAGCGA; sh-YTHDF1: UUAUUCUCUUGUCCUUUUGUU; sh-YTHDF2: UCAAGUAAGGUUCGAAAUCAU) sequences of the target genes were designed and synthesized. Subsequently, the amplified sequences were inserted into lentiviral vectors (LV6 was used as the overexpression vector and LV-1 as the knock-down vector), and positive clones were confirmed by sequencing to obtain recombinant plasmids. Tool vector plasmids carrying target genes and helper plasmids (for lentivirus packaging) were transfected into 293T cells by GenePharma and cultured for 6 h. The medium was then replaced with complete medium. Seventy-two hours later, cell supernatants were collected, purified, and condensed. The acquired liquid was subjected to a viral titer test at 108 TU/ml.
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5

Silencing AKR1B10 Expression via shRNA

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The AKR1B10-targeting shRNA and its negative control shRNA (shNC) constructed in the LV2 lentiviral vector, and lentiviral particles expressing luciferase infused shRNA were packaged in 293T cells (GenePharma, Suzhou, China). The sequences of shRNAs were 5’-CACGCATTGTTGAGAACAT-3’(sh1) and 5’-GTGCCTATGTCTATCAGAA-3’ (sh2). The target sequences of AKR1B10 plasmid were referred to its genetic sequence in the PubMed (https://www.ncbi.nlm.nih.gov/gene). Transfection was carried out as directed by the manufacturer. The knockdown or overexpression efficiency was validated by western blot analysis.
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6

Generating A549 Cell Xenograft Model

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A549 cells with stable sh-circ_0017109 expression were generated by lentiviral transduction. pLKO.1-Puro lentiviral vector with circ_0017109 shRNA or scramble control shRNA (sh-NC) was provided by Genomeditech Co., Ltd. (Shanghai, China). The production of lentivirus was conducted in 293 T cells by GenePharma Co. Ltd. (Shanghai, China). Cells infected with lentivirus were selected with 800 ng/mL puromycin for 2 weeks before inoculation. Adult BALB/c nude mice (~ 25–30 g) were provided by National Resource Center for Mutant Mice of China (Nanjing, China). Nude mice were raised in a controlled environment at 22 °C with 12 h light/dark cycle. The animals were assigned to two groups (n = 6 each). To establish mouse xenograft model of NSCLC, each mouse was injected with 2 × 106 A549 cells (stable expression of circ_0017109 shRNA or sh-NC) in PBS (150 μL) subcutaneously via flanks. Tumor size was measured every week using a caliber. After 4 weeks, euthanasia of mice was performed using 20% of carbon dioxide in a closed chamber for 15 min until no movement was observed. Tumor was then dissected for subsequent analysis. All the animal experimental protocols were conducted in compliance with animal use and care guidelines of Tianjin Medical University Cancer Institute and Hospital, and were approved by the corresponding animal experimental committee.
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7

Transfection of 293T cells with miR-6132

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293T cells were obtained from Procell Life Science & Technology Co., Ltd (Wuhan, China). 293T cells were transfected with miR-6132 mimics, inhibitor or respective negative control (GenePharma, Shanghai, China). The transfected cells were cultured in RPMI 1640 culture medium and harvested for 24 h. The sequences used in this study are listed in Table 2.
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8

Predicting miR-125 Binding to CDK2

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TargetScan (targetscan.org/vert_72/) was used to predict the binding sites between miR-125 and CDK2. According to the prediction, wild-type (wt) and mutant (mut)-type sequences of the binding sites between miR-125 and CDK2 were synthesized and cloned into the reporter vectors (pGL3-Basic, Promega Corporation), which were named mut-CDK2 and wt-CDK2. 293T cells (American Type Culture Collection) were co-transfected with mut-CDK2 or wt-CDK2 and miR-125 mimic, miR-125 inhibitor, NC mimic or NC inhibitor (GenePharma, Shanghai, China). OPTI-MEM (49 µl) was pipetted onto 24-well plates to dilute 1 µl Lipofectamine 2000 reagent (Invitrogen; Thermo Fisher Scientific, Inc.), and the final volume was 50 µl. After 48 h transfection, luciferase activity was detected using a Lucifer Reporter analytic system (Promega Corporation) by comparison with Renilla luciferase activity.
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9

Stable Knockdown of lncRNA ELFN1-AS1 in SW1990 Cells

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A specific SW1990 cell line (SW1990-LNC-KD) with the stable knock down of lncRNA ELFN1-AS1 and a scramble control SW1990 cell line were constructed with lnc-small hairpin RNA (shRNA) or a scramble control (see Table S1) cloned into the pLV3 (H1/GFP & Puro) vector (see Figure S1) and transfected into 293T cells (Shanghai GenePharma China). Supernatants were collected after 72 h incubation and used for the transfection (24 h incubation before transfection) of the SW1990s (12 (link)). SW1990 cells containing the lnc-shRNA were screened by media containing 5 µg/mL puromycin (Sigma, St. Louis, MO, USA), and used for the Xenograft tumor growth experiments (13 (link)).
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10

Culturing H1299 and 293T Cells

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H1299 cells were obtained from the American Type Culture Collection (Manassas, VA, USA), while 293T cells for cell transfection purchased from Gene Pharma (China). The cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; high glucose) supplemented with 10% fetal bovine serum (Bioind, USA) and 1% penicillin/streptomycin (Solarbio, Beijing, China) in a humidified atmosphere with 5% CO2 at 37°C. The transfection reagent Lipofectamine 2000 was purchased from Vigorous Biotechnology (China). Plasmids for cell transfection were provided and constructed by a laboratory.
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