KEY RESOURCESTABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit polyclonal anti-GFP, Alexa Flour 488 | Invitrogen | Cat#A-21311; PRID: AB_221477 |
| Goat polyclonal anti-GFP | Rockland | Cat#600-101-215; PRID: AB_218182 |
| Rabbit polyclonal anti-dsRed | Clontech | Cat#632496; PRID: AB_10013483 |
| Bacterial and Virus Strains | ||
| AAVretro-EF1a-Cre-WPRE | Salk Viral Core GT3 | N/A |
| scAAVretro-hSyn1-H2B-eGFP | Salk Viral Core GT3 | N/A |
| scAAVretro-hSyn1-H2B-mCherry | Salk Viral Core GT3 | N/A |
| AAVretro-CAG-FLEXloxp-Flp | Salk Viral Core GT3 | N/A |
| AAV8-CAG-FLEXfrt-TVAmCherry-WPRE | Salk Viral Core GT3 | N/A |
| AAV8-CAG-FLEXfrt-oG-WPRE | Salk Viral Core GT3 | N/A |
| AAV8-CAG-FLEXloxp-oG-WPRE | Salk Viral Core GT3 | N/A |
| AAV8-EF1a-FLEXloxp-eGFP-2A-TVA-WPRE | Salk Viral Core GT3 | N/A |
| AAVretro-nef-lox66/71-tTA | Salk Viral Core GT3 | N/A |
| AAV8-TRE-DIO-oG-WPRE | Salk Viral Core GT3 | N/A |
| AAV8-TRE-DIO-TVAmCherry-WPRE | Salk Viral Core GT3 | N/A |
| EnvA+RVdG-eGFP | Salk Viral Core GT3 | N/A |
| EnvA+RVdG-dsRed2 | Kim et al., 2015 | N/A |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Cholera Toxin Subunit B, Alexa Fluor 488 conjugated | Molecular Probes | Cat#C22841 |
| Cholera Toxin Subunit B, Alexa Fluor 555 conjugated | Molecular Probes | Cat#C22843 |
| Cholera Toxin Subunit B, Alexa Fluor 647 conjugated | Molecular Probes | Cat#C34778 |
| DL-Dithiothreitol | Sigma | Cat#646563; CAS: 3483-12-3 |
| Protease inhibitor | Sigma | Cat#P8340 |
| RNasin Plus RNase inhibitor | Promega | Cat#N2611 |
| Dylight 647-Lectin | Vectorlabs | Cat#DL-1178 |
| DAPI (4’,6-Diamidino-2-Phenylindole, Dihydrochloride) | Thermo Fisher | Cat#D1306; CAS: 28718-90-3 |
| Hoechst 33342 | Thermo Scientific | Cat#PI62249; CAS: 23491-52-3 |
| Triton X-100 | Thermo Fisher | Cat#AC327371000; CAS: 9002-93-1 |
| Chlorprothixene | Sigma | Cat#C1671; CAS: 6469-93-8 |
| Isoflurane | MWI Veterinary Supply | Cat#502017; CAS: 26675-46-7 |
| Critical Commercial Assays | ||
| SMART-Seq v4 Ultra Low Input RNA Kit | Clontech | Cat#634894 |
| Nextera XT DNA Library Preparation Kit | Illumina | Cat#FC-131-1024 |
| RNAscope Fluorescent Multiplex Assay kit | ACD Biosciences | Cat#320850 |
| Ampure XP beads | Ampure XP beads | Cat#A63880 |
| Deposited Data | ||
| Single-nuclei RNA sequencing datasets | This manuscript | GSE133230 |
| Mouse reference genome mm10 (GENCODE M10) | UCSC Genome Browser | http://genome.ucsc.edu/cgibin/hgGateway?db=mm10 |
| Experimental Models: Organisms/Strains | ||
| Mouse: INTACT: B6.129-Gt(ROSA)26Sortm5(CAGSun1/sfGFP)Nat/MmbeJ | The Jackson Laboratory | JAX: 030952 |
| Mouse: SepW1-Cre NP39 | MMRRC | MMRRC: s037622-UCD |
| Mouse: Tlx3-Cre PL56 | MMRRC | MMRRC: 036547-UCD |
| Mouse: Wildtype: C57BL/6J | The Jackson Laboratory | JAX: 000664 |
| Oligonucleotides | ||
| RNAscope Mm-Astn2 probe | ACD Biosciences | Cat#523871-C3 |
| RNAscope Mm-Kcnh5 probe | ACD Biosciences | Cat#497691-C2 |
| RNAscope Mm-Grm1 probe | ACD Biosciences | Cat#449781-C2 |
| RNAscope Mm-Cntn5 probe | ACD Biosciences | Cat#567461-C3 |
| Recombinant DNA | ||
| pAAV-CAG-FLEXloxp-Flp | Ren et al., 2018 | N/A |
| pAAV-CAG-FLEXfrt-TVAmCherry-WPRE | Schwarz et al., 2015 | N/A |
| Software and Algorithms | ||
| Cutadapt [v2.3] | Martin, 2011 | https://cutadapt.readthedocs.io/en/v2.3/develop.html |
| STAR [v2.5.1b] | Dobin et al., 2013 | https://github.com/alexdobin/STAR |
| Picard DownsampleSam [v1.130] | Picard | http://broadinstitute.github.io/picard/ |
| Homer [v4.8] | Heinz et al., 2010 | http://homer.ucsd.edu/homer/ |
| Seurat [v2.3.4] | Butler et al., 2018 | https://satijalab.org/seurat/ |
| Zinbwave [v1.4.1]-EdgeR [v3.20.9] | Butler et al., 2018 | https://bioconductor.org/packages/devel/bioc/vignettes/zinbwave/inst/doc/intro.html |
| Zinbwave [v1.4.1]-DESeq2 [v1.20.0] | Butler et al., 2018 | https://github.com/mikelove/zinbwave-deseq2 |
| Terastitcher | Bria and Iannello, 2012 | https://github.com/abria/TeraStitcher |
| reorg4terastitcher.py | Puifai Santisakultarm | N/A |
| FIJI | NIH ImageJ software | https://fiji.sc/ |
| CellSense | Olympus | N/A |
| Zen | Zeiss | N/A |
| Prism 7.0e | GraphPad | N/A |
| R [v3.5.1] | The R Project | https://www.r-project.org/ |
| Customized Matlab code for intrinsic signal imaging | Garrett and Nauhaus et al., 2014 | https://snlc.github.io/ISI/ |
| Imaris | Oxford Instruments | N/A |
| Other | ||
| BD Influx for FANS | BD Biosciences | N/A |
| HiSeq 4000 | Illumina | N/A |
| Picospritzer | General Valve Corp | N/A |
| BX63 microscope | Olympus | N/A |
| LSM780 microscope | Zeiss | N/A |
| VF-300 compresstome™ | Precisionary Instruments | N/A |
| SZX16 dissection microscope | Olympus | N/A |
| Leica CM 1950 cryostat | Leica | N/A |
| Z.1 lightsheet microscope | Zeiss | N/A |
| Airyscan 880 | Zeiss | N/A |