KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rat monoclonal anti-HA | Roche/Sigma | Cat#11867423001 |
| Rabbit polyclonal anti-HA | Sigma | Cat#H6908 |
| Mouse monoclonal anti-HA | BioLegend | Cat#MMS-101P |
| Mouse monoclonal anti-HA Agarose | ThermoFisher (Pierce) | Cat#26181 |
| Rabbit polyclonal anti-Myc | Santa Cruz | Cat#sc-789 |
| Mouse monoclonal anti-V5 | ThermoFisher | Cat#R960-25 |
| Chicken polyclonal anti-GFP | Abcam | Cat#ab13970 |
| Rabbit polyclonal anti-mCherry | Abcam | Cat#ab167453 |
| Rabbit polyclonal anti-MAP2 | Synaptic Systems | Cat#188002 |
| Mouse monoclonal anti-Ankyrin G | Santa Cruz | Cat#sc-12719 |
| Rabbit polyclonal anti-βIV-Spectrin | ThermoFisher | Cat#PA5-62972 |
| Guinea pig polyclonal anti-VGAT | Synaptic Systems | Cat#131004 |
| Guinea pig polyclonal anti-Synapsin I | Synaptic Systems | Cat#106104 |
| Mouse monoclonal anti-βIII-tubulin | Sigma | Cat#T8660 |
| Rabbit polyclonal anti-GAPDH | Abcam | Cat#ab9485 |
| Goat anti-mouse Alexa 405 | ThermoFisher | Cat#A31553 |
| Donkey anti-rat Alexa 488 | ThermoFisher | Cat#A21208 |
| Goat anti-chicken Alexa 488 | ThermoFisher | Cat#A11039 |
| Goat anti-rabbit Alexa 555 | ThermoFisher | Cat#A21428 |
| Goat anti-rat Alexa 568 | ThermoFisher | Cat#A11077 |
| Goat anti-rabbit Alexa 568 | ThermoFisher | Cat#A11036 |
| Goat anti-guinea pig Alexa 594 | ThermoFisher | Cat#A11076 |
| Goat anti-rat Alexa 594 | Jackson ImmunoResearch | Cat#112-585-167 |
| Donkey anti-rabbit Alexa 647 | ThermoFisher | Cat#A31573 |
| Donkey anti-mouse Alexa 647 | Jackson ImmunoResearch | Cat#715-605-150 |
| Goat anti-mouse Alexa 647 | Jackson ImmunoResearch | Cat#115-605-166 |
| Donkey anti-guinea pig Alexa 647 | Jackson ImmunoResearch | Cat#706-605-148 |
| Goat anti-mouse Atto 647N | Sigma | Cat#50185 |
| Goat anti-rat IRDye 800CW | LI-COR | Cat#925-32219 |
| Goat anti-rabbit IRDye 800CW | LI-COR | Cat#926-32211 |
| Goat anti-rabbit IRDye 680RD | LI-COR | Cat#926-68071 |
| Bacterial and Virus Strains | ||
| E. coli NEB Stable | NEB | Cat#C3040 |
| E. coli One Shot Stbl3 | ThermoFisher | Cat#C737303 |
| AAV2/1 encapsulated HiUGE vectors | This paper | N/A |
| AAV2/9 encapsulated HiUGE vectors | This paper | N/A |
| AAV2-retro encapsulated HiUGE vectors | This paper | N/A |
| Biological Samples | ||
| N/A | ||
| Chemicals, Peptides, and Recombinant Proteins | ||
| D-AP5 | Tocris | Cat#0106 |
| Cytosine arabinoside | Sigma | Cat#C1768 |
| Polyethylenimine (PEI) | Polysciences | Cat#24765 |
| Benzonase | Novagen | Cat#70664 |
| Lipofectamine 3000 | ThermoFisher | Cat#L3000008 |
| Normal goat serum | Sigma | Cat#G9023 |
| Optiprep density gradient | Sigma | Cat#D1556 |
| Critical Commercial Assays | ||
| BCA protein assay | Pierce | Cat#23227 |
| InFusion cloning kit | TaKaRa | Cat#638910 |
| TOPO TA Cloning Kit for Sequencing | ThermoFisher | Cat#K457501 |
| CanGetSignal solution | TOYOBO | Cat#NKB-101T |
| MyTaq Extraction-PCR kit | Bioline | Cat#BIO-21127 |
| PureLink Genomic DNA Mini Kit | ThermoFisher | Cat#K182001 |
| DNeasy Blood & Tissue Kit | Qiagen | Cat#69504 |
| MyTaq HS Mix | Bioline | Cat#BIO-25045 |
| MyTaq HS Red Mix | Bioline | Cat#BIO-25047 |
| PowerUp SYBR Green Master Mix | ThermoFisher | Cat#A25741 |
| SensiFAST Real-Time PCR Kit | Bioline | Cat#BIO-86005 |
| Genome Walker kit | Clontech | Cat#636406 |
| Amicon Ultra-15 filtration unit | Millipore | Cat#UFC910008 |
| Spin-X centrifuge tube filter | Costar | Cat#8162 |
| Deposited Data | ||
| N/A | ||
| Experimental Models: Cell Lines | ||
| HEK293T cells | ATCC | CRL-11268 |
| NIH3T3 cells | ATCC | CRL-1658 |
| HeLa cells | ATCC | CCL-2 |
| Experimental Models: Organisms/Strains | ||
| Mouse: Gt(ROSA)26Sortm1(CAG-cas9*,-EGFP)Fezh | Jackson Laboratory | 024857 |
| Mouse: C57BL/6J | Jackson Laboratory | 000664 |
| Oligonucleotides | ||
| Donor Recognition Sequences (DRS), see Table S1 | This paper | N/A |
| Guide RNA (gRNA) targets, see Table S1 | This paper | N/A |
| Donor sequences, see Table S1 | This paper | N/A |
| Primers, see Table S1 | This paper | N/A |
| Recombinant DNA | ||
| AAV:ITR-U6-sgRNA(backbone)-hSyn-Cre-2A-EGFP-KASH-WPRE-shortPA-ITR | Feng Zhang (Platt et al., 2014) | Addgene Plasmid #60231 |
| pAAV-nEFCas9 | Juan Belmonte (Suzuki et al., 2016) | Addgene Plasmid #87115 |
| rAAV2-retro helper | Alla Karpova & David Schaffer (Tervo et al., 2016) | Addgene Plasmid #81070 |
| pCAG-smFP HA | Loren Looger (Viswanathan et al., 2015) | Addgene Plasmid #59759 |
| pAAV-HiUGE-GS-gRNA vectors | This paper | N/A |
| pAAV-HiUGE-Donor vectors | This paper | N/A |
| pAAV-HiUGE-GS-gRNA vectors with intein-split-Cas9 | This paper | N/A |
| pAAV-HiUGE-Donor vectors with intein-split-Cas9 | This paper | N/A |
| Software and Algorithms | ||
| FIJI | (Schindelin et al., 2012; Schneider et al., 2012) | https://fiji.sc |
| CRISPOR | (Haeussler et al., 2016) | http://crispor.tefor.net |
| Cas-OFFinder | (Bae et al., 2014) | http://www.rgenome.net/cas-offinder |
| Trim Galore Toolkit (v 0.5.0) | Babraham Bioinformatics | http://www.bioinformatics.babraham.ac.uk/projects/trim_galore |
| Trimmomatic | (Bolger et al., 2014) | http://www.usadellab.org/cms/?page=trimmomatic |
| Cutadapt (v 1.18) | (Martin, 2011) | https://pypi.org/project/cutadapt/ |
| FastQC (v 0.11.5 or v 0.11.8) | Babraham Bioinformatics | https://www.bioinformatics.babraham.ac.uk/projects/fastqc |
| bwa-mem (v0.7.17) | (Li and Durbin, 2009) | https://sourceforge.net/projects/bio-bwa/files/ |
| SAMtools (v1.9) | (Li et al., 2009) | https://github.com/samtools/samtools |
| Picard | Broad Institute | http://broadinstitute.github.io/picard |
| GATK HaplotypeCaller (v3.8-1-0-gf15c1c3ef) | (McKenna et al., 2010) | https://software.broadinstitute.org/gatk/ |
| FLASH | (Magoc and Salzberg, 2011) | https://ccb.jhu.edu/software/FLASH/ |
| EMBOSS Needle | (Chojnacki et al., 2017) | https://www.ebi.ac.uk/Tools/psa/emboss_needle/nucleotide.html |
| CRISPResso | (Pinello et al., 2016) | http://crispresso.rocks/ |
| R | The R Foundation | https://www.r-project.org/ |
| JMP Pro | SAS | https://www.jmp.com |
| Other | ||
| Zeiss LSM 880 | Zeiss | N/A |
| Zeiss LSM 710 | Zeiss | N/A |
| Zeiss Imager.M2 with Apotome.2 | Zeiss | N/A |
| Leica STED microscope | Leica | N/A |
| Odyssey Fc Imager | LI-COR | N/A |