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9 protocols using paav mcs

1

Generating Customized AAV Vectors

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To produce adeno-associated virus (AAV) vectors, ND1-P2A-mCherry was inserted into pAAV-FLEX-GFP vector (Addgene) to replace GFP to generate pAAV-Flex-CAG-ND1-P2A- mCherry. mCherry was inserted into pAAV-FLEX-GFP to replace GFP and was used as a negative control. Human GFAP promoter (1.6 kb) was inserted into pAAV-MCS (Cell Biolabs) to replace CMV promoter, then Cre was subcloned into pAAV-MCS to generate pAAV-hGFAP-Cre. The backbone of pAAV-GFAP::ND1-GFP and pAAV-GFAP::GFP vectors is pAAV-MCS (Cell Biolabs, Inc.). CMV promoter was changed to GFAP promoter, and GFP or NeuroD1-GFP was inserted to MCS. Recombinant AAV9 was produced by HEK293T cell line. The purification method used Iodixanol Gradient Solutions (D1556, Optiprep, Sigma) and desalting and concentrating on Merck Amicon Ultra-15 Centrifugal Filters (UFC910008, Millipore). Purified AAV viruses were titered using QuickTiter AAV Quantitation Kit (VPK-145, Cell biolabs).
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2

Collagen II T-cell Epitope Synthesis

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Previously characterized CII T-cell epitopes were synthesized in a sequence derived from the native murine collagen II (Col2A1) gene cDNA sequence by Genescript (Piscataway, NJ). The resulting construct was cloned via Gibson assembly (New England Biolabs, Rowley, MA) into either pAAV-MCS or pacAd5 CMV K-N (all from Cell Biolabs, San Diego, CA) to generate the pAAV-MCS: CII or pacAd5 CMV K-N: CII constructs.
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3

Recombinant AAV Vectors for GRK2 Expression

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Recombinant AAV vectors that expressed, under the influence of the Myh11 promoter, either the GRK2 or the GFP that served as the infection control were generated. We selected AAV-DJ8 as a virus serotype in this study after the vasculature expression trial of GFP with Myh11 promotor. The Grk2 gene and Myh11 promoter were cloned from a wildtype C57BL/6 J mouse that was purchased from Clea Japan (Tokyo, Japan). The GFP-expressing plasmid was procured from Cell Biolabs (AAV-400, San Diego, California, United States). For pAAV-DJ8-GRK2 or pAAV-DJ8-GFP plasmid construction, pAAV-MCS were purchased from Cell Biolabs (VPK-410). After inserting Grk2 or GFP and exchanging CMV promotor to Myh11 promotor in pAAV-MCS, it was transfected into human embryonic kidney 293 cells together with pAAV-DJ8 and pHelper purchased from Cell Biolabs (VPK-420-DJ-8, 3402-02) to produce AAV-DJ8-GRK2 or AAV-DJ8-GFP vector. The vector was then purified, and concentrated by two cycles through the Amicon Ultra-15 centrifugal filters (UFC910024; Merck Millipore, Burlington, Massachusetts, United States). The purified viral preparations were stored in phosphate-buffered saline, and physical particle titers were determined using competitive PCR. The primers used for cloning Grk2 gene and Myh11 promoter are listed in S1 Materials and Methods.
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4

Recombinant AAV Production for Mitochondrial Biosensors

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pLPCX mito-roGFP-Orp1 (Addgene; #64992) was digested with XhoI/ClaI, blunted and cloned into pAAV-MCS (Cell Biolabs, Inc.) under the control of a CMV promoter. Clones were validated by sequencing. Likewise, pcDNA-mito-ATeam (from H. Imamura, Tokyo, Japan) was digested with XhoI/HindIII, blunted and cloned into the CMV promoter controlled pAAV-MCS. Mitochondria-targeting tags were CoxVIII for roGFP-Orp1 and two tandem copies of CoxVIII for mito-ATeam. AAV viral particles were produced at the viral vector production centre at the Centre de Biotecnologia Animal I Teràpia Gènica in Barcelona, Spain or the University of Nantes, France.
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5

Generating Recombinant AAV Constructs

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pAAV-Laconic and pAAV-δGlu6 were obtained by digesting Laconic/pcDNA3.1(-) (gift from Luis Felipe Barros; Addgene plasmid #44238) [25 (link)] and pcDNA3.1 FLII12Pglu-700uδ6 (gift from Wolf Frommer; Addgene plasmid # 17866) [26 (link)] by BamH1/HindIII (NEB) and cloned into pAAV-MCS (Cell Biolabs, Inc.) under of a CMV promoter. Clones were validated by sequencing. pcDNA-mito-AT1.03 (from H. Imamura, Tokyo, Japan) [27 (link)] was digested with XhoI/HindIII (NEB), blunted and cloned into the CMV promoter controlled pAAV-MCS. Mitochondria-targeting tags were two tandem copies of CoxVIII. pAAV9 were produced at UPV, Universitat Autonoma de Barcelona or at INSERM U1089 University of Nantes, France.
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6

Generation of Gene-Editing Tools and Vectors

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TALENs were assembled by GoldenGate cloning following guidelines from published work.46 (link) The plasmid kit used for generation of TALENs was a gift from Daniel Voytas and Adam Bogdanove (Addgene kit # 1000000024). For generation of mRNA, TALEN-containing fragments were subcloned into the cloning vector pWNY.47 (link) TALEN mRNA was generated using the mMESSAGE mMACHINE T7 transcription kit (#AM1344, Thermo Fisher Scientific) for small-scale preparations or was purchased as a large amount (Trilink Biotechnologies, San Diego, CA). ZFNs targeting CCR5 in NHP cells have previously been described.12 (link) For CRISPR/Cas9, 20 μg purified Cas9 mRNA (Trilink Biotechnologies, San Diego, CA) was combined with 600 pmol chemically modified guide RNA (5′-GCATGTGACAGGTGAGGCAC-3′; Synthego, Redwood City, CA) targeting CD33 exon 2. The BCL11A donor insert was assembled by fusion PCR and cloned into the ClaI/SpeI restriction sites of plasmid pAAV-MCS (#VPK-411, Cell Biolabs, San Diego, CA). BCL11A donor serotype 5 AAV was prepared by the Kiem laboratory Vector Core services following a standard procedure involving transfection of packaging cells with a three-plasmid system.
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7

Recombinant AAV Packaging Protocols

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A Venus-luciferase 2 reporter gene cassette (ffLuc-cp156, gifted from Dr. Atsushi Miyawaki at RIKEN) was inserted into pAAV-MCS (Cell Biolabs, San Diego, CA, USA), which contains AAV2 ITRs, the CMV promoter, the human β-globin intron and the human growth hormone polyadenylation signal. Plasmids containing both Rep and Cap genes for AAV serotypes 1, 2, 3, 4, 5, and 6 were purchased from Cell Biolabs. To package the recombinant AAVs, including serotypes 7, 8, 9, and rh10, sequence information for each Cap gene was obtained from GenBank (NC_006260, NC_006261, AY530579 and AY243015, respectively) and was further synthesized (Eurofins Genomics, Tokyo, Japan). The synthesized DNA fragments were subsequently subcloned into the AAV Rep-Cap plasmid (Cell Biolabs).
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8

Generation of Codon-Optimized AIPL1 AAV Vectors

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Protein coding sequence of human AIPL1 (AF148864.2) was retrieved from GenBank. Codon optimization was performed using EMBOSS backtranseq and verified with the Graphical Codon Usage Analyser [65 ]. AIPL1 codon-optimized (Supplementary Figure S1) and wild-type sequences were synthesized by Topgenetech (Montréal, QC, Canada) and then recloned into pAAV-MCS (Cat. number VPK-400, Cell Biolabs, San Diego, CA, USA) to produce pAAV-AIPL1co and pAAV-AIPL1wt. In addition, AIPL1 sequences were fused with His-tag and also cloned in pAAV-MCS to generate pAAV-AIPL1co-His and pAAV-AIPL1wt-His. The pAAV-GFP (Cat. number VP-401, Cell Biolabs, USA) was used as a transfection control. The pAAV-RC2/9 (AddGene, 112865, Watertown, MA, USA) and pHelper (Part No. 340202, Cell Biolabs Inc., San Diego, CA, USA) with pAAV-AIPL1co and pAAVAIPL1wt, were used to produce AAV vectors.
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9

Plasmid Construction for Cell Signaling

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If not otherwise specified, all plasmids expressing FKBP or FRB were constructed by standard subcloning techniques based on either pECFP, pEYFP and pmCherry plasmids (Clonetech). Human Plaat cDNAs were purchased from ORIGENE [RC208444 for PLAAT1 (NM_020386), RC212578 for PLAAT2 (NM_017878), RC200242 for PLAAT3 (NM_007069), RC201923 for PLAAT4 (NM_004585), and RC228184 for PLAAT5 (NM_054108)]. For construction of pAAV-CMV-YFP-FKBP-18TM, pAAV-CMV-YFP-FKBP-18TM-LD, and pAAV-CMV-TOM20-CFP-FRB, pAAV-MCS (Cell Biolabs) was digested with EcoRI and BamHI, and fragments of YFP-FKBP-18TM, YFP-FKBP and TOM20-CFP-FRB were inserted to the digested sites using In-Fusion Snap Assembly Master Mix (Takara Bio USA, 638947). To visualize Golgi, lysosomes, autophagosomes, endosomes and nuclear membrane, Giantin S, Lamp1, and Su9 cDNA were inserted to pECFP and cDNAs of Lc3, Rab5, and Lamin A were inserted to pmCherry by standard subcloning technique. Parkin cDNA was also subcloned to pEYFP. For PEX3-CFP-FRB, cDNAs encoding human PEX3, mCerulean3 and FRB were inserted into pcDNA3.1(+) (Invitrogen) vector by standard restriction enzyme subcloning. mScarlet-SRL29 (link) was obtained from Addgene (#85065). All plasmids were verified by Sanger sequencing.
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