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31 protocols using pgfp 5 rs

1

Culturing Human Liver Cancer Stem Cells

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Human liver cancer stem cell line (hLCSC) was maintained in Dulbecco's modified Eagle medium (Gibco BRL Life Technologies) or Minimum Essential Medium (MEM) (Gibco BRL Life Technologies) supplemented with 10% heat-inactivated fetal bovine serum (Gibco) in a humidified atmosphere of 5% CO2 incubator at 37°C. pGFP-V-RS, pCMV6-A-GFP, were purchased from Origene (USA);pGFP-V-RS-HOTAOR, pCMV6-A-GFP-HOTAIR, pcDNA3.1-STED2 were constructed by ourselves.
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2

Obtaining Recombinant Reelin from Stable Cell Line

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Reagents involved in cell cultures were purchased from Thermo Fisher Scientific. Pharmacological inhibitors including rapamycin, rapalogs and other chemical inhibitors were purchased from LC Laboratories. Stable cell line CER was used to obtain the recombinant reelin in the conditioned medium as described [32] (link), and the corresponding mock medium was obtained from the parental 293 EBNA cell line as described [31] (link). Maf1 specific 29mer shRNA constructs were expressed from retroviral GFP vector (pGFP-V-RS) (OriGene). Maf1 shRNA and scramble shRNA were expressed from AAV-PHP.eB vectors (PackGene Biotech). Vector overexpressing Myc-tagged Maf1 was constructed from pCMV6-AN-His-Myc vector (OriGene). Raptor shRNA was expressed from pLKO.1 vector (AddGene). Antibodies and other experimental reagents used in this study can be found in Table S3.
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3

Stable Knockdown of Notch1 in Lung Cancer Cells

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Plasmids encoding human Notch1 shRNA, empty vector (pGFP‐V‐RS), and TurboFectin 8.0 transfection reagent, were purchased from OriGene Technologies (Rockville, MD, USA). PC‐9 and H1975 cells were divided equally into two groups: shNotch1 (transfected with Notch1 shRNA) and shControl (transfected with empty vector) cells. The day prior to transfection, cells were seeded at a density of 1 × 105/well onto six‐well plates. Then, the cells were transfected with 2 μg Notch1 shRNA plasmid or blank vector in serum‐free Opti‐MEM I (Thermo Fisher Scientific) using 6 μl TurboFectin 8.0. After 24 h, the transfected cells were diluted 1:10 in 10‐cm dishes and the culture medium was replaced with complete medium containing puromycin (Sigma‐Aldrich). Stably positive clones were obtained after screening with puromycin.
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4

HOXA9 Overexpression and Silencing

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U87MG and hTERT/E6/E7 were previously retrovirally infected with MSCVneo vectors containing HOXA9 cDNA [16 (link)]. For HOXA9 silencing, GBML18 and U251 cells were transfected with pGFP-V-RS plasmid containing HOXA9-specific shRNAs or non-effective shRNAs sequences (Origene).
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5

Investigating Mitosis and Virus Replication

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To explore the role of Tpr, p53, and CDK1 in the regulation of mitosis and virus replication, Vero or DF-1 cells at 75% confluence were transfected with gene-specific shRNAs targeting Tpr, p53, CDK1, scrambled shRNA (29-mer non-effective scrambled pGFP-V-RS vector), and pGFP-V-RS vector, respectively. All the shRNAs and scrambled shRNAs (TR30013) were obtained from OriGene Co. (Rockville, USA) and constructed in the vector pGFP-V-RS (TR30007). Each shRNA kit containing four different shRNA sequences, targeting the respective genes, was tested in Vero cells. The one resulting in the most significant down regulation of respective protein expression was chosen and used in this study (Table 1).
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6

Syntenin Knockdown and Rescue

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RNAis targeting Syntenin and the non-targeting control RNAi (si Ctrl) were purchased from GE healthcare Dharmacon Inc (Human syntenin (5′-GCAAGACCUUCCAGUAUAA-3′), Mouse syntenin smartpool (M-043821-01)). For rescue experiments, syntenin cDNA was cloned in pcDNA3.1/Zeo(+) (Thermofisher Scientific) and mutated by directed mutagenesis on three nucleotides in the sequence targeted by the siRNA (CCTTCCAGT mutated to CCGTCGAGC).
Empty vector, control shRNA and the 29 mer human and mouse shRNA sequences cloned in pGFP-V-RS vector were purchased from Origene [control shRNA GCACTACCAGAGCTAACTCAGATAGTACT (TR30013), Human syntenin shRNA 2 (GCCTAATGGACCACACCATTCCTGAGGTT (TG309594B/GI338370), shRNA 3 (GTGGCTCCTGTAACTGGTAATGATGTTGG (TG309594C/GI338371), Mouse shRNA (TCAGGCTCAAACTGCTTATTCTGCCAATC (TG512166A/GI574570)].
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7

Lentiviral Transduction of SIRT1 shRNA

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The shRNA-expressing lentiviral vector pGFP-V-RS against the SIRT1 gene was obtained from Origene (cat. #: TG309433; Rockville, MD, USA). The virus particles were harvested 48 h after transfecting 293FT cells. The cells were grown in 6-well plates at 60–70% confluency, and 1 mL of viral supernatant was added with 1 μL Polybrene for a stable transfection.
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8

Knocking Down IKZF1 in Nalm6 Cells

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The Nalm6 cells were transiently transfected with human IKZF1 shRNA constructs in the GFP vector (pGFP-v-RS) (Origene) using the Neon Transfection System (Invitrogen, USA). We used ascrambled 29-mer shRNA cassette in the pGFP-v-RS vector as a control. Knockdown of IKZF1 was confirmed by measurement of IKZF1 mRNA level with qPCR [14 (link), 16 (link), 27 (link)]. Primers: IKZF1-F: 5′-GGCGCGGTGCTCCTCCT-3′, IKZF1-R: 5′-TCCGACACGCCCTACGACA-3′.
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9

Plasmid Amplification and Purification

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Plasmids carrying reporter genes for either green fluorescent protein (GFP, pGFP-V-RS) or red fluorescent protein (RFP, pRFP-C-RS) were purchased from OriGene (Rockville, MD). Plasmids were amplified in E. coli and isolated using a mega prep kit purchased from Qiagen (cat#: 12181). DNA working solutions used for cartridge preparation were diluted to 1 μg/μL in TE.
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10

Hep3B Cell Maintenance and Plasmid Constructs

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Human liver cancer line Hep3B was maintained in DMEM Medium supplemented with 10% heat-inactivated fetal bovine serum (Gibco) in a humidified atmosphere of 5% CO2 incubator at 37 °C. Plasmid pGFP-V-RS, pCMV6-A-GFP, pCMV6-XL5-PTEN, pGFP-V-RS-PTEN, pGFP-V-RS-Sirt1, pMiR-Target were purchased from Origene (Rockville, MD 20850, USA). pEZX-MT01-PTEN-3’UTR was purchased from GeneCopeia (Rockville, MD, USA).pCMV6-AC-GFP-HULC [the HULC sequence (NR_004855) was synthesized and cloned into the cloning site ofpCMV6-AC-GFP plasmid (Origene)], pcDNA3-sirt1[the Sirt1 sequence in the Flag-SIRT1 (Plasmid #1791,Addigene) was digested and subcloned into the cloning site of pcDNA3], pcDNA3-sirt mutant [the mutant Sirt1 (H363Y) sequence in the Flag-SIRT1 H363Y (Plasmid #1792, addigene) was digested and sub-cloned into the pcDNA3] were constructed by our lab.
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