KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| chicken anti-RFP 1:200 | Rockland | Cat# 600-901-379S, RRID:AB_10703148 |
| mouse anti-RFP 1:200 | Rockland | Cat# 200-301-379S, RRID:AB_2611064 |
| rabbit anti-RFP 1:200 | Rockland | Cat# 600-401-379S, RRID:AB_11182807 |
| rabbit anti-5-HT 1:200 | Immunostar | Cat# 20080, RRID:AB_572263 |
| rabbit anti-Tph2 1:500 | Millipore | Cat# ABN60, RRID:AB_11212793 |
| mouse anti-Tph2 1:500 | Millipore | Cat# MAB5278, RRID:AB_11214093 |
| rabbit anti-AADC 1:200 | Millipore | Cat# AB1569, RRID:AB_90789 |
| mouse anti-GFAP 1:500 | Sigma | Cat# G3893, RRID:AB_477010 |
| rabbit anti-Iba1 1:500 | FUJIFILM | Cat# 019-19741, RRID:AB_839504 |
| rabbit anti-COX4 1:500 | Thermo Fischer | Cat# PA5-29992, RRID:AB_2547466 |
| chicken anti-beta 3 tubulin 1:500 | Novus Biologicals | Cat# NB100-1612, RRID:AB_10000548 |
| rabbit anti-Sert 1:400 | Immunostar | Cat# 24330, RRID:AB_572209 |
| guinea pig anti-Synapsin1 1:500 | Synaptic Systems | Cat# 106 104, RRID:AB_2721082 |
| mouse anti-Synaptotagmin1 1:500 | Sigma | Cat# SAB1404433, RRID:AB_10759362 |
| mouse anti-Gephyrin 1:500 | Synaptic Systems | Cat# 147 011, RRID:AB_887717 |
| rabbit anti-α-Synuclein 1:500 | Cell Signaling | Cat# 2642, RRID:AB_2192679 |
| rabbit anti-APP 1:500 | Sigma | Cat# SAB4300464, RRID:AB_10621836 |
| mouse anti-P-Neurofilament 1:500 | BioLegend | Cat# SMI-31P-100, RRID:AB_2028812 |
| rat anti-CD68 1:500 | BIO RAD | Cat# MCA1957, RRID:AB_322219 |
| Goat anti-Mouse, Alexa 647 1:500 | Thermo Fisher Scientific | Cat# A-21240, RRID:AB_2535809 |
| Goat anti-Rabbit, Alexa 647 1:500 | Thermo Fisher Scientific | Cat# A-21246, RRID:AB_2535814 |
| Goat anti-Rabbit, Alexa 594 1:500 | Thermo Fisher Scientific | Cat# A-11012, RRID:AB_2534079 |
| Goat anti-Mouse, Alexa 594 1:500 | Thermo Fisher Scientific | Cat# A-21155, RRID:AB_2535785 |
| Goat anti-Chicken, Alexa 594 1:500 | Thermo Fisher Scientific | Cat# A32759, RRID:AB_2762829 |
| Goat anti-Rabbit, Alexa 488 1:500 | Thermo Fisher Scientific | Cat# A-11070, RRID:AB_2534114 |
| Goat anti-Mouse, Alexa 488 1:500 | Thermo Fisher Scientific | Cat# A-21131, RRID:AB_2535771 |
| VECTASTAIN ABC-Peroxidase Kit | Vector Laboratories | Cat# PK-4001, RRID:AB_2336810 Cat# PK-4004,RRID:AB_2336813 Cat# PK-4002, RRID:AB_2336811 Cat# PK-4007, RRID:AB_2336816 |
| Anti-Digoxigenin-AP Fab Fragments | Roche | Cat# 11093274910, RRID:AB_2734716 |
| Bacterial and virus strains | ||
| pENN.AAV.CMVs.PI.Cre.rBG | PennVector/ADDGENE | RRID:Addgene_105537 |
| Chemicals, peptides, and recombinant proteins | ||
| Protease | Sigma | Cat# P8811 |
| bupivacaine HCL | Hospira | Cat# C0409-3613-01 |
| Meloxicam | Pfizer | Cat# 71125-38-7 |
| Tamoxifen | Sigma | Cat# T5648 |
| PCA | Sigma | Cat# 274763 |
| 8-OH-DPAT | Tocris | Cat# 87394874 |
| D-AP5 | Tocris | Cat# 0106 |
| DNQX | Tocris | Cat# 0189 |
| TTX | Abcam | Cat# ab120054 |
| TRIZOL LS | Ambion | Cat# 10296010 |
| Chloroform | Fisher Scientific | Cat# C298500 |
| NBT | Roche | Cat# 11383213001 |
| BCIP | Roche | Cat# 11383221001 |
| Formimide | Roche | Cat# 11814320001 |
| Critical commercial assays | ||
| PerfeCTa PreAmp Supermix | QuantaBio | Cat# 89409170 |
| PerfeCTa FastMix II ROX Mastermix | QuantaBio | Cat# 97065990 |
| RNA Clean and Concentrator kit | ZYMO | Cat# R1013 |
| Ovation® SoLo RNA-Seq Library Preparation Kit | Tecan (Nugen Inc.) | Cat# 040732 |
| CORT ELISA kit | ENZO Life Sciences | Cat# 101106156 |
| Transcriptor First Strand cDNA Kit | Roche | Cat# 04896866001 |
| Deposited data | ||
| Lmx1b & Pet1 CUT&RUN and histone mark ChIPmentation | https://doi.org/10.1101/2021.10.13.463782 | GSE185737 |
| Raw and analyzed data | This paper | GSE189052 |
| Experimental models: Organisms/strains | ||
| Mouse: Tph2-CreERT2 | Jackson Laboratory | RRID:IMSR_JAX:016584 |
| Mouse: Lmx1bflox | Jackson Laboratory; PMID:17151281 | Stock # 031287; RRID:MGI:3810753 |
| Mouse: Pet1flox | PMID:20818386 | RRID:MGI:4837213 |
| Mouse: Tph2flox | Jackson Laboratory; PMID:24972638 | RRID:IMSR_JAX:027590 |
| Mouse: Pet1-Cre | Jackson Laboratory; PMID:16251278 | Stock #012712; RRID:MGI:4837211 |
| Mouse: Ai9 RosaTdTom | Jackson Laboratory | Stock #: 007909; RRID:MGI:4436851 |
| Oligonucleotides | ||
| Tph2 Probe | TaqMan | Cat# Mm00557722 |
| Pet1 Probe | TaqMan | Cat# Mm00462220 |
| Ddc Probe | TaqMan | Cat# Mm00516688 |
| Slc6a4 Probe | TaqMan | Cat# Mm00439391 |
| Software and algorithms | ||
| MATLAB | https://www.mathworks.com/products/matlab.html | RRID:SCR_001622 |
| Fiji/ImageJ | https://imagej.net/Fiji | RRID:SCR_002285 |
| FASTQC | https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ | RRID:SCR_014583 |
| Trimmomatic | Bolger et al., 2014 | RRID:SCR_011848 |
| Hisat2 (v2.1.0) | Kim et al., 2019 | RRID:SCR_015530 |
| Cufflinks v2.2.2 | Trapnell et al., 2010 | RRID:SCR_014597 |
| Webgestalt | http://www.webgestalt.org | RRID:SCR_006786 |
| Imaris 7.4.2 | http://www.bitplane.com/ | RRID:SCR_007370 |
| Filament Analysis 19 Beta | Matthew J. Gastinger | https://github.com/Ironhorse1618/Python3.7-Imaris-XTenstions/blob/master/XT_MJG_Filament_Analysis19_beta.py |
| PClamp | Molecular Devices | RRID:SCR_011323 |
| ANY-maze | Stoelting | RRID:SCR_014289 |
| Video Freeze software | Med Associates | RRID:SCR_014574 |
| Integrated Genome Viewer v2.9.3 | https://software.broadinstitute.org/software/igv/ | RRID:SCR_011793 |
| bamCoverage function v3.5.0 | https://deeptools.readthedocs.io/en/develop/ | RRID:SCR_016366 |
| Prism 8.0 | https://www.graphpad.com/scientific-software/prism/ | RRID:SCR_002798 |
| Huygens Deconvolution | Scientific Volume Imaging http://svi.nl | RRID:SCR_014237 |
| ggpubr | https://rdocumentation.org/packages/ggpubr/versions/0.4.0 | RRID:SCR_021139 |
| pheatmap | https://www.rdocumentation.org/packages/pheatmap/versions/0.2/topics/pheatmap | RRID:SCR_016418 |
| DEXSeq | http://bioconductor.org/packages/release/bioc/html/DEXSeq.html | RRID:SCR_012823 |
| ENCODE | https://www.encodeproject.org/ | RRID:SCR_015482 |
| Bowtie 2 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml | RRID:SCR_016368 |
| samtools | http://htslib.org/ | RRID:SCR_002105 |
| SEACR | https://seacr.fredhutch.org/ | Meers et al., 2019 |
| BEDTools | https://github.com/arq5x/bedtools2 | RRID:SCR_006646 |
| GREAT | http://great.stanford.edu/public/html/splash.php | RRID:SCR_005807 |
| MEME suite | http://meme-suite.org/ | RRID:SCR_001783 |
| MACS2 | https://github.com/macs3-project/MACS | RRID:SCR_013291 |
| ENCODE ChIP-seq processing pipeline | https://github.com/ENCODE-DCC/chip-seq-pipeline2/ | RRID:SCR_021323 |
| ChIPSeqSpikeInFree | https://github.com/stjude/ChIPseqSpikeInFree | https://doi.org/10.1093/bioinformatics/btz720 |
| Other | ||
| Microvette | Sarstedt | Cat# 201278100 |
| Plastic Feeding Tubes | Instech | Cat# FTP2225 |
| Artificial Tears | CWRU Animal Resource Center Henry Schein |
Cat# 11695-68321 |
| FBS | Gibco | Cat# 10439024 |
| Corn Oil | Sigma | Cat# C8267 |
| VetBond (webglue) | CWRU Animal Resource Center Patterson Veterinary |
Cat# 078910065 |
| OCT solution | Fisher Scientific | Cat# 23730571 |
| MAS-GP Adhesive Glass Slides | Matsunami | Cat# 10748176 |
| Betadine | Emerson Healthcare Llc. | Cat# 19027132 |
| 20X SSC | Fischer BioReagents | Cat# BP13251 |