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14 protocols using paav dj

1

Purification of Recombinant AAV Vectors

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Three plasmids, an AAV vector, pAAV-DJ (Cell Biolabs, San Diego, CA, USA) and pHelper were transfected into 80–90% confluent AAV293 cells (Cell Biolabs). After 3 days of incubation, cells were harvested. AAV vectors produced in AAV293 cells were purified by CsCl (Nacalai Tesque) gradient ultracentrifugation using a SW41Ti rotor (Beckman-Coulter Life Science, Indianapolis, IN) at 35,000 rpm for 72 h at 16 °C. The formed gradients were fractionated, and the AAV titer of each fraction was evaluated by qPCR (TOYOBO, Osaka, Japan). AAV-rich fractions were combined and dialyzed using a dialysis cassette Slide-A-Lyzer (Thermo Fisher Scientific) to remove CsCl. The final AAV titer was determined by qPCR.
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2

Site-Specific Gene Integration Using AAV

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The pAAV/HBV were kindly provided by Pei-Jer Chen (National Taiwan University) 20.
pcDNA3.1/HBV, pAAV-C4371, pAAV-Y1021, pAAV-Y10 were constructed in the State Key
Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen University. The
constructs and molecular and phenotypic characteristics were described in our previous
report 52. pAAV/DJ (Cell Biolabs, Inc. San Diego, CA, USA), a cloning vector expressing
the rep/cap of AAV, can mediate the site-specific integration of an exogenous gene when
co-injected with the pAAV expression vector. All plasmids were amplified in DH5α E. coli
and purified using a Qiagen plasmid Maxi kit (endo-free).
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3

AAV Packaging Utilizing Hybrid Vectors

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pscAAV was purchased from Cell Biolabs, Inc. We obtained 13 hybrid pAAV-Rep-Cap (pAAV-RC) vectors, which encode the rep of AAV2 and variable cap genes of different serotypes. Among them, pAAV2-RC was purchased from Stratagene, pAAV-RC3B, pAAV-RC4, pAAV-RC6 and pAAV-DJ were purchased from Cell Biolabs, and pAAV2/1, pAAV2/5 JC, pAAV2/7, pAAV2/8, pAAV9n, pAAV2/rh10, pAAV2/hu11 and pAAV2/rh32.33 were obtained from Penn Vector Core of the University of Pennsylvania. For AAV packaging, the pHelper plasmid (Stratagene) and AAVpro-293T cells (Clontech) were used.
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4

AAVV Production for miR-199a-3p Expression

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To obtain an AAVV expressing miR-199a-3p, all the plasmids required for AAVV generation (pAAV-IRES-GFP, pAAV-DJ, and pHelper) were purchased from Cell Biolabs (San Diego, CA, USA). The cassette expressing the miR-199a-3p sequence was obtained from the pIRES-miR-199a plasmid50 (link) and cloned upstream of the IRES-GFP sequence into pAAV-IRES-GFP using XbaI sites. The infectious recombinant AAVV-199 was generated by a 1:1:1 (molar ratio) triple transfection of pAAV-199 with helper plasmids (pAAV-DJ and pHelper) into 293FT cells. Viral production and titration were performed as previously reported.51 (link)
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5

Viral Vectors for Neuronal Labeling and Manipulation

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pAAV-EF1a-DIO-mCherry (Addgene plasmid# 50462; http://n2t.net/addgene:50462; RRID: Addgene_50462) was a gift from Bryan Roth. pAAV-phSyn1(S)-FLEX-tdTomato-T2A-SypEGFP-WPRE was a gift from Hongkui Zeng (Addgene plasmid# 51509; http://n2t.net/addgene:51509; RRID: Addgene_51509) (Oh et al., 2014 (link)). pAAV-EF1a-FLEX-TVA-mCherry was a gift from Naoshige Uchida (Addgene plasmid# 38044; http://n2t.net/addgene:38044; RRID: Addgene_38044) (Watabe-Uchida et al., 2012 (link)). pAAV-FLEX-SADcvsG was generated (Mori and Morimoto, 2014 (link)). For recombinant AAV (rAAV) production, the vectors were cotransfected into HEK293 cells with pAAV-DJ (Cell Biolabs, San Diego, CA, USA) and pHelper (Takara Bio Inc., Shiga, Japan) using AAVpro Helper-Free system (Takara Bio Inc.). rAAV particles were extracted and purified using the AAVpro Purification Kit (Takara Bio Inc.), according to the instructions of the manufacturer. rAAV titers were determined by quantitative PCR using the AAVpro Titration Kit (Takara Bio Inc.), and aliquoted rAAVs were stored at −80°C.
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6

AAV Production Protocols

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AAV production was performed as previously described.29 (link) In brief, an AAV vector plasmid (pAAV-CAG-mCherry, pAAV-CAG-Kitl or pAAV-CAG-Cre), an adenovirus helper plasmid (pHelper; Agilent Technologies, Santa Clara, CA), and an AAV helper plasmid (pAAV-RC; Agilent Technologies, pAAV1, pAAV6.2, pAAV9; gift from Penn Vector Core [University of Pennsylvania, PA], pAAV-DJ, pAAV-DJ8; Cell biolabs, San Diego, CA, and pAAV-7M8; Addgene, Boston, MA) were transiently transfected into 293T cells. Viral titers (in vector genomes (VG)/mL) were determined by real-time PCR using FastStart Universal SYBR Green Master Mix (Roche Diagnostic GmbH, Penzberg, Germany) and specific primers, as described previously (Watanabe et al., 2018). For screening, the titer of the virus was 1 × 1012 vector genomes/mL. In some experiments, we also used AxCAN-Egfp (RIKEN BRC), CSII-EF1-IRES-Venus (RIKEN BRC) and CSII-EF1-Kitl. The titer of AxCAN-Egfp was 2.0 × 108 plaque-forming units/mL. The titers of CSII-EF1-IRES-Venus and CSII-EF1-Kitl were 1.5 × 109 transducing units (TU)/mL and 2.8 × 109 TU/mL, respectively.
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7

Recombinant AAV Production in HEK293T

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HEK293T cells were seeded in 15 cm dishes and transfected at 80–90% confluence. GFP-AAV plasmid, N-ABE-AAV or C-ABE-AAV were transfected along with pHelper and pAAV-DJ from the AAV-DJ Packaging System from Cell Biolabs in a 1:1:1 ratio using calcium phosphate and a total of 60 µg per plate. Media was replaced 24 h post transfection. Cell pellets were harvested at 72 h post transfection through manual cell scraping and centrifuged at 1500×g for 12 min. After aspirating the supernatant, the cell pellet was resuspended in 1 mL AAV lysis buffer (50 mM Tris-HCl pH = 8.5, 150 mM NaCl and 2 mM MgCl2). Resuspended pellets were subjected to three freeze–thaw cycles between an ethanol/dry ice bath and a 37 °C water bath. Lysed cell pellets were then spun at 10,000×g for 10 min and the supernatant was collected as crude lysate. Lysates were then treated with 50 U benzonase per mL and incubated at 37 °C for 30 min to digest unpackaged plasmid. Crude lysates were added directly to cells or flash frozen with liquid nitrogen and stored at −80 °C for future use.
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8

Lentivirus and AAV Production for Neuronal Transduction

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Lentivirus was prepared as described previously (Zhang et al., 2009 (link)). HEK293FT cells (Life Technologies) were transfected with FUGW-H1 with LH4 shRNA, psPAX2 (a gift from Dr. Didier Trono through Addgene, #12260) and pVSVG (Stewart et al., 2003 (link)) using the calcium phosphate method. After overnight incubation, medium was changed, and cells were incubated 36–40 hrs. Then supernatant was collected, filtered and concentrated by ultracentrifugation (80,000 g for 2 hours at 4 °C). The viral pellet was resuspended in PBS and stored at −80 °C. Neurons were infected with lentivirus at DIV3.
Adeno-associated virus (AAV) was prepared as described previously (McClure et al., 2011 (link)). Briefly, three plasmids of pAAV-DJ, pHelper (Cell Biolabs, Inc.) and AAV-U6-sgRNA-pCBh-Cre encoding LH4 sgRNAs were co-transfected into 293AAV cells (Cell Biolab, Inc.) using the calcium phosphate method. 48–60 hours after transfection, cells were solubilized and AAVs were purified using a HiTrap Heparin column (GE healthcare).
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9

Circadian Rhythms Monitoring via CRE-Luc2P Assay

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A luciferase reporter driven by a tandem repeat of the Gpr19 CRE sequence (3 × CRE-Luc2P) was inserted between the ITR sequences of pAAV-MCS vector (Cell Biolabs Inc) to obtain pAAV-3 × CRE-Luc2P. HEK293T cells cultured in dish were co-transfected with pAAV-3 × CRE-Luc2P, pAAV-DJ, and pHelper according to the manufacturer's instructions (Cell Biolabs Inc). Three days after transfection, cells were harvested and resuspended in 1 ml of DMEM, followed by four freeze–thaw cycles and centrifugation. The titers of 3 × CREwt-Luc2P and 3 × CREmut-Luc2P virus solutions were ~ 8 × 1012 genome copies/mL. The SCN slices were prepared according to our standard method59 (link). Two days after the preparation of SCN slices, the AAV solution (3 μL per slice) was inoculated on the surface of the SCN slices. Infected slices were further cultured for ~ 14 days. Thereafter, luminescence from the culture was measured with a dish-type luminometer (Kronos Dio, ATTO) at 35 °C using 1 mM luciferin59 (link). The luminescence was monitored for 2 min at 20-min intervals for each slice. The raw data were smoothed using a 1-h moving average and further detrended by subtracting a 24 h running average.
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10

Production and Purification of Recombinant AAVs

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AAVs carrying hGFAP::Cre and CAG::FLEx-GFP for serotype testing in human islets were as previously described.58 (link) AAV8-U6-mINS2utr5sg-EGFP-2cut (6.15 × 1013 GC/mL) was produced and purified by Penn Vector Core. AAV-DJ-U6-mINS2utr5sg-EGFP-2cut (2.92 × 1012 GC/mL), AAV-DJ-U6-hINSin1sg-CopGFP-2cut (1.83 × 1013 GC/mL), AAV-DJ-U6-hINSin1sg-CopGFP-1cut (6.02 × 1012 GC/mL), and AAV-DJ-nEF-Cas9 (3.83 × 1012 GC/mL) were produced and purified as described below. Briefly, recombinant AAVs were produced in 293 AAV cells (Cell Biolabs, San Diego, CA, USA). Polyethylenimine (PEI, linear, MW 25,000) was used for transfection of three plasmids: the pAAV vector constructs, pAAV2/8-RC (Penn Vector Core) or pAAV-DJ (Cell Biolabs), and pHelper (Cell Biolabs). At 72 h post-transfection, cells were scrapped in their medium, centrifuged, and then frozen and thawed four times by placing alternately in dry ice-ethanol and a 37°C water bath to lyse the cells and release the virus. The resulting AAV crude lysate was purified by centrifugation at 54,000 rpm for 1 h in discontinuous iodixanol gradients with a Beckman SW55Ti rotor. The virus-containing layer was extracted, and viruses were concentrated by Millipore Amicon Ultra Centrifugal Filters (Millipore-Sigma, Bedford MA, USA). Virus titers were determined by quantitative PCR (qPCR) according to Addgene protocol.
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