KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Chicken polyclonal anti-GFP | Abcam | Cat# ab13970; RRID: AB_300798 |
| Rabbit polyclonal anti-GFP | Millipore | Cat# AB3080P; RRID: AB_2630379 |
| Mouse polyclonal anti-Isl1 | DSHB | Cat# 39.4D5; RRID:AB_2314683 |
| Goat polyclonal anti-Choline Acetyltransferase | Millipore | Cat# AB144P; RRID: AB_11214092 |
| Goat polyclonal anti-Vesicular Acetylcholine Transporter | Millipore | Cat# ABN100; RRID: AB_2630394 |
| Goat polyclonal anti-Sox-2 (Y-17) | Santa Cruz | Cat# sc-17320; RRID: AB_2286684 |
| Rabbit polyclonal anti-Dsred | Living Colors | Cat# 632496; RRID: AB_10013483 |
| Chicken polyclonal anti-GFP | AVES | Cat# GFP-1020; RRID: AB_10000240 |
| Rabbit monoclonal anti-HA | Cell Signaling | Cat# 3724s; RRID: AB_1549585 |
| Mouse monoclonal anti-actin, clone C4 | Millipore | Cat# MAB1501; RRID: AB_2223041 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Ames’ Medium | Sigma | Cat# A1420 |
| Papain | Worthington | Cat# LS003126 |
| Ovomucoid | Worthington | Cat# LS003087 |
| AzuraQuant cDNA synthesis kit | Azura | Cat# AZ-199 |
| DAPI (4’,6-Diamidino-2-Phenylindole, Dihydrochloride) | Life Technologies | Cat# D1306; RRID: AB_2629482 |
| Lipofectamine 2000 Transfection Reagent | ThermoFisher Scientific | Cat# 11668019 |
| Critical Commercial Assays | ||
| Chromium Single Cell 3′ Library & Gel Bead Kit v2, 16 rxns | 10X Genomics | Cat# 120237 |
| Chromium Single Cell A Chip Kit, 16 rxns | 10X Genomics | Cat# 1000009 |
| Chromium i7 Multiplex Kit 96 rxns | 10X Genomics | Cat# 120262 |
| Smart-seq2 reagents | Picelli et al., 2014 | N/A |
| Nextera XT DNA Library Preparation Kit | Illumina | Cat# FC-131–1024 |
| RNAscope Fluorescent Multiplex Kit | Advanced Cell Diagnostics | Cat# 320850 |
| RNAlater | ThermoFisher | Cat# AM7024 |
| RNeasy Mini Kit | QIAGEN | Cat# A74104 |
| RNAclean SPRI | Beckman Coulter Genomics | Cat# A63987 |
| RNAscope® Probe- eGFP | Advanced Cell Diagnostics | Cat# 400281 |
| RNAscope® Probe- GFP-C2 | Advanced Cell Diagnostics | Cat# 409011-C2 |
| RNAscope® Probe- Mm-Chat-C3 | Advanced Cell Diagnostics | Cat# 410071-C3 |
| RNAscope® Probe- Mm-Megf10-C3 | Advanced Cell Diagnostics | Cat# 406641-C3 |
| RNAscope® Probe- Mm-Rnd3-C2 | Advanced Cell Diagnostics | Cat# 424731-C2 |
| RNAscope® Probe- Mm-Gfra3-C2 | Advanced Cell Diagnostics | Cat# 467191-C2 |
| RNAscope® Probe- Mm-Slit2-C2 | Advanced Cell Diagnostics | Cat# 449691-C2 |
| RNAscope® Probe- Mm-Tenm3 | Advanced Cell Diagnostics | Cat# 411951 |
| RNAscope® 3-plex Negative Control Probe | Advanced Cell Diagnostics | Cat# 320871 |
| RNAscope® 3-plex Positive Control Probe Mm | Advanced Cell Diagnostics | Cat# 320881 |
| NEBuilder® HiFi DNA Assembly Cloning Kit | New England BioLabs | Cat# E5520S |
| Phusion® Hot Start Flex 2X Master Mix | New England BioLabs | Cat# M0536S |
| SuperScript™ III First-Strand Synthesis SuperMix | ThermoFisher | Cat# 18080400 |
| TRIzol™ Plus RNA Purification Kit | ThermoFisher | Cat# 12183555 |
| Deposited Data | ||
| Raw data files for scRNA-sequencing | This study | GEO: GSE132555 |
| Raw data files for RNA-sequencing | This study | GEO: GSE132555 |
| Experimental Models: Organisms/Strains | ||
| Mouse: Fezf1:eGFP | Gift from B. Chen | N/A |
| Mouse: B6.Cg-Tg(Thy1-EYFP)15Jrs/J | Buffelli et al., 2003 | Stock#: 005630; RRID: IMSR_JAX:005630 |
| Mouse: CD1 | Charles River | 022 |
| Mouse: Megf10:Cre | This paper | N/A |
| Mouse: B6.129(Cg)-Gt(ROSA)26Sortm4(ACTB-tdTomato,-EGFP)Luo/J | Jackson Laboratory | Stock#: 007676, RRID: IMSR_JAX:007676 |
| Experimental Models: Cell Lines | ||
| Cell line: HEK293T cells | ATCC | Cat# CRL-3216; RRID: CVCL_0063 |
| Bacterial and Virus Strains | ||
| AAV9-hSyn1–3XHA-Fezf1-P2A-eGFP (4.01E+13) | Janelia Research Campus Viral Tools | N/A |
| AAV9-CAG-TdTomato (4.01E+13) | UNC Vector Core | N/A |
| AAV9-DsRed-shScrambled ((4.01E+13) | Janelia Research Campus Viral Tools | N/A |
| AAV9-hSyn1-DsRed-shRnd3 (4.8393E+13) | Janelia Research Campus Viral Tools | N/A |
| AAV9-hSyn1-DsRed-shScrambled (4.8393E+13) | Janelia Research Campus Viral Tools | N/A |
| Recombinant DNA | ||
| pCIG2 | Hand et al., 2005 | N/A |
| pCIG2-LSL-3xHA-Fezf1 | This study | N/A |
| pCIG2-LSL-3xHA-Rnd3 | This study | N/A |
| pCAG-Cre | Hand et al., 2015 | N/A |
| pPRIME-DsRed-shScramble | This study | N/A |
| pPRIME-DsRed-shRnd3 | This study | N/A |
| pAAV-hSyn1-MCS | This study | N/A |
| pAAV-hSyn1–3xHA-Fezf1-P2A-eGFP | This study | N/A |
| pAAV-hSyn1-DsRed-shScramble | This study | N/A |
| pAAV-hSyn1-DsRed-shRnd3 | This study | N/A |
| Oligonucleotides see Table S1 | ||
| Software and Algorithms | ||
| Cell Ranger v2.1.0 | 10X genomics | https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest |
| Tophat | Trapnell et al., 2012 | RRID: SCR_013035 |
| Cufflinks | Trapnell et al., 2012 | http://cole-trapnell-lab.github.io/cufflinks/; RRID: SCR_014597 |
| Cuffdiff | Trapnell et al., 2012 | http://cole-trapnell-lab.github.io/cufflinks/; RRID: SCR_001647 |
| R version 3.4.1 | The R project | https://www.r-project.org/ |
| ImageJ | NIH | http://rsb.info.nih.gov.ezp-prod1.hul.harvard.edu/ij/index.html; RRID:SCR_003070 |
| Pairwise stitching ImageJ plugin | NIH | http://imagej.net/Image_Stitching |
| Segmentation Simple Neurite Tracer ImageJ plugin | NIH | http://imagej.net/Simple_Neurite_Tracer |
| DRP | Rockhill et al., 2000 | http://wvad.mpimf-heidelberg.mpg.de/abteilungen/biomedizinischeOptik/software/WinDRP/index.html |
| Zen | Zeiss | RRID:SCR_013672 http://www.zeiss.com/microscopy/en_us/products/microscope-software/zen.html#introduction |
| Other | ||
| Illumina Nextseq 500 | Illumina | N/A |
| Illumina Hiseq | Illumina | N/A |