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Genejet plasmid maxiprep kit

Manufactured by Thermo Fisher Scientific
Sourced in United States

The GeneJET Plasmid Maxiprep Kit is a laboratory tool designed for the efficient isolation and purification of high-quality plasmid DNA from bacterial cultures. It utilizes a silica-based membrane technology to yield large amounts of plasmid DNA suitable for a variety of downstream applications.

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30 protocols using genejet plasmid maxiprep kit

1

Lentiviral Transfer Plasmid for IL-15/IL-15Rα

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The pHR’ lentiviral transfer plasmid was used as a template to produce a lentiviral transfer plasmid that encodes IL-15/IL-15Rα. The construct contains a murine Igκ-signal peptide, the IL-15 sequence (NCBI Reference Sequence: NP_000576.1) and was connected via a P2A self-cleaving site to a Igκ-signal peptide followed by the IL-15Rα sequence (NCBI Reference Sequence: NP_002180.1) and a hemagglutinin (HA)-tag.
The gene fragments were designed in silico using SnapGene (Dotmatics, USA) and subsequently codon optimized using the IDT codon optimization tool. We added 3’ and 5’ sequences that were homologous to the pHR’ plasmid insertion site and ordered the synthetic gene fragments (gBlocks, Integrated DNA Technologies, USA). The transfer plasmid was opened with restriction enzymes EcoRI and BamHI (Thermo Fisher Scientific, USA) and the gBlocks were ligated using the NEBuilder HiFi DNA Assembly mix (New England Biolabs, USA). Competent bacteria (New England Biolabs) were transformed, expanded and plasmid DNA was isolated using the GeneJET Plasmid Maxiprep Kit (Thermo Fisher Scientific). Quantities of plasmid DNA were evaluated using a spectrophotometer.
The lentiviral transfer plasmids encoding K2-Fc or R3-Fc21 (link), an antibody-variant of the nanobody that binds the idiotype of 5T2 myeloma cells (R3B23)22 (link), were previously described.
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2

Gateway Cloning of Plasmids

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The plasmids pT3-IRES-GFP, pT3-FAK-IRES-GFP, pT3-FAK (K454R)-IRES-GFP, pT3-CAT, and pT3-MET were generated by Gateway cloning as described.(9 (link),10 (link)) The plasmids were purified using GeneJET Plasmid Maxiprep Kit (Thermo Fisher Scientific) for hydrodynamic tail vein injection.
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3

Amplification and cloning of pri-miR-181c-5p

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The sequence of pri-miR-181c-5p was amplified from the genomic DNA of human Peripheral Blood Mononuclear Cells (PBMCs), extracted by QIAamp genomic DNA kit (QIAGEN, USA), using Thermo Scientific DreamTaq Green PCR master mix (Thermo Fisher Scientific, Waltham, MA, USA) and forward primer: 5′-TCGA-GGATCC- ACTTAAGGAGCGGGCTTGAG-3′ and reverse primer: 5′-TCGA-GCTAGC- TCACAACCCACCGACAACA-3′, according to the manufacturer’s instruction. The PCR for pri-miR-181c-5p amplification was carried out as follows: 95 °C for 5 min; and 35 cycles of 94 °C for 15 s, 54 °C for 30 s, and 72 °C for 30 s. The amplified product was subsequently cloned in a pEGP-miR vector to form pmiR-181c-5p with the aid of Thermo Scientific T4 DNA ligase (Thermo Fisher Scientific, Waltham, MA, USA). The cloned constructs were transformed subsequently into the cells of Escherichia coli TOP10 and confirmed by sequencing. Following the manufacturer’s guidelines, the verified clone was purified by an endotoxin-free GeneJET Plasmid Maxiprep Kit from Thermo Scientific (Thermo Fisher Scientific, Waltham, MA, USA). The Thermo Fisher Scientific Nanodrop 2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) was used to measure the concentration and purity of the pmiR-181c-5p construct. The pEGP-miR null vector (pNull) was considered a control vector.
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4

Stable GCN2 Knockdown using shRNA

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Stable shRNA-mediated GCN2 knockdown was achieved using pLKO.1 cloning vector (Addgene, Cambridge, MA, USA) with GFP replacing the puromycin insert. Briefly, pLKO stuffer was released upon digestion with EcoRI and AgeI (New England Biolabs, MA, USA). Oligos were annealed and ligated into the pLKO.1, producing a final plasmid expressing the shRNA of interest (shGCN2(1), shGCN2(2), and non-targeting shNTC (Supplementary Table 1)). DH5α cells (New England Biolabs) were transformed with ligation mix and plated on LB agar plates containing ampicillin. Positive clones were identified by sequencing with a pLKO.1 sequencing primer (5′ CAA GGC TGT TAG AGA GAT AAT TGG A 3′). Maxi prep using GeneJet Plasmid Maxiprep Kit (ThermoFisher) was carried out to produce large-scale quantities of the plasmid. Lentiviral particles were generated with HEK-293T (GenHunter) to carry out the viral transfection using X-treme Gene HP kit (Roche, Switzerland). Transfection efficiency was confirmed after 48 h; 72 h post-transfection virus was collected by ultracentrifugation. A549 cells were transduced and GFP-positive cells were sorted by FACS.
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5

Functionalization of Gold Surfaces

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Triethylene glycol mono-11-mercaptoundecyl ether (PEG-thiol), nickel (II) sulfate hexahydrate, sodium, chloride, potassium hexacyanoferrate (III) and ethanolamine HCL were purchased from Sigma-Aldrich, ethanol (200 proof) from Decon Laboratories LLC, 2-{2-[2-(1-mercaptoundec-11-yloxy)-ethoxy]-ethoxy)-ethoxy nitrilotriacetic acid (NTA-thiol) from ProChimia Surfaces, Poland and potassium ferrocyanide trihydrate from Acros Organics. N-hydroxysuccinimide (NHS), N-(3-dimethylaminopropyl)-N′-ethylcarbodiimide hydrochloride (EDC) and GeneJET Plasmid Maxiprep Kit were received from Thermo-Scientific. All other reagents were purchased from VWR international, Randor, PA, USA. Solutions were prepared using deionized (DI) water (~18 MΩ) (Ultra Purelab system, ELGA/Siemens or Milli-Q Direct 8 water system). The polycrystalline gold chips (50 nm Au over 2.5 nm titanium adhesion layers, coated on 18mm × 18mm cover slip glass slides) were purchased from Platypus Technologies, LLC, Madison, WI and each chip was cut into two halves before further processing.
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6

cDNA Overexpression in SH-SY5Y and HEK293T

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The cDNA encoding full length RP11–677M14.2 was PCR-amplified from undifferentiated SH-SY5Y (ASNrgnHindIII_Fw 5’-CGAAGCTTCTTTCAGTACCAGGATTCTTTGGG-3’; ASNrgnXhoI_Rev 5’-CGCTCGAGAGGTACGTAATAGCTTTATTTTGGGG-3’) and subcloned into pcDNA3.1 vector (Invitrogen). The empty pcDNA3.1 vector was used as the control. All plasmids were isolated using GeneJET Plasmid Maxiprep kit (ThermoFisher) and the specific clones were confirmed by DNA sequencing of at least 5 colonies. HEK293T and SH-SY5Y (500.000 cells) were transfected with 1mg of proviral construct using 3 mL PolyJet transfection reagent (SignaGen Laboratories) per manufacturer’s instructions. The assays were conducted 24–48 hrs after transfection.
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7

Site-Directed Mutagenesis Protocol

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Point mutations, as described in the text, were cloned using the Q5 Site-Directed Mutagenesis Kit (New England Biolabs, Ipswich, MA, USA) per manufacturer’s protocol using primer sequences indicated in the supplemental methods. Clones were confirmed with sequencing by Eton Bioscience (San Diego, CA, USA). Plasmids were maxiprepped using GeneJET Plasmid Maxiprep Kit (Thermo Fischer Scientific, Waltham, MA, USA) per manufacturer’s protocol.
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8

Cloning of Ribosomal Protein L5

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The GeneJET PCR Purification Kit (Thermo Fisher Scientific, Lithuania) was used to purify the PCR product containing the ribosomal protein L5 coding sequence, as per the manufacturer's instructions. Double digest with EcoR1 plus XbaI was applied on purified L5-cDNA and the pCI mammalian expression vector (Promega, United States). T4 DNA ligase (Thermo Fisher Scientific, Lithuania) was used to ligate digested L5-cDNA with the pCI mammalian expression vector. pCI-L5 clones were transformed into E. coli TOP10. Recombinant plasmids were extracted from transformed E. coli TOP10 by alkaline sodium dodecyl sulphate (SDS) lysis and a column purified of endotoxins (GeneJET Plasmid Maxiprep Kit; Thermo Fisher Scientific, Lithuania) according to the manufacturer's instructions.
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9

Plasmid-Enabled Protein Expression Protocols

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The plasmids detailed in Table 2 were used for mammalian cell transfection to express human proteins, or expression in E. coli for protein purification. GeneJET Plasmid Maxiprep kit (Thermo Fisher Scientific; Waltham, MA, USA) was used for plasmid purification.

Plasmids

Protein or tagPlasmidTagExpressionSupplier, reference
EZH2pCMV6Myc-DDKMammalianOrigene, #RC202054
Flag-ØpCEFLFlagMammalianGift from JS Gutkind (NIH)
GST-ØpGEX-2TKGSTBacterialGE Healthcare GE28-9546-53
HA-ØpCEFLHAMammalianGift from JS Gutkind (NIH)
HDAC1pcDNA3.1+FlagMammalianAddgene, #13820
KDM1A (LSD1)pCMV6Myc-DDKMammalianOrigene, #RC208480
KDM3A (JMJD1A)pLentiV5-MycMammalianAddgene, #82331
KDM4A (JMJD2A)pCMVHAMammalianAddgene, #24180
PCAFpClFlagMammalianNakatani [81 (link)]
SETDB1pIRES2-EGFPFlagMammalianRodriguez Paredes [82 (link)]
VRK1pCEFLHAMammalianValbuena et al. [83 (link)]
VRK1pcDNA3.1MycMammalianValbuena et al. [83 (link)]
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10

Expression and Purification of VRK1, SIRT1, and SIRT2

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Plasmid pCEFL-HA-VRK1 was used to express human VRK1 [32 (link),50 (link)] and pcDNA3.1-Flag-SIRT1 and pcDNA3.1-Flag-SIRT2 plasmids were used to express human SIRT1 and SIRT2 [13 (link),51 (link)]. GeneJET Plasmid Maxiprep kit (Thermo Fisher Scientific, Waltham, MA, USA) was used for plasmid purifications.
For in vitro kinase assays, PGEX-4T-VRK1-GST, pGEX-4T-VRK1[K179E]-GST, pGEX-2T-p53[1-84]-GST and pET30a-SIRT2-6xHis plasmids [13 (link),46 (link),50 (link)] were used for expression and purification of the fusion proteins expressed in Escherichia coli strain BL21. Protein expressions were induced with IPTG 0.2 M 37 °C for 2 h and bacteria were lysed with lysis buffer (20 mM Tris HCl pH 8.0, NaCl 500 mM, 1% Triton X-100, 0.025% NaN3, 0.2 μg/mL lysozyme and 5 mM DTT) or BC-500 buffer (20 mM Tris pH 8.0, 100 mM NaCl, 10 mM EDTA pH 8.0, 0.1% NP40 and 2% sarkosyl). The resulting GST or His fusion proteins were incubated with Glutathione Sepharose 4B beads (GE Healthcare Systems; Chicago, IL, USA) or NiNTA Agarose beads (Qiagen; Hilden, Germany), respectively. After several washes with the corresponding lysis buffer, the proteins were obtained by elution with glutathione 20 mM or imidazole 50 mM. Purified proteins were aliquoted and stored at −80 °C.
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