KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Chemicals, Peptides, and Recombinant Proteins | ||
| Anisomycin from Streptomyces griseolus | Sigma-Aldrich | Cat#A9789 |
| Pronase | Sigma-Aldrich | Cat#10165921001 |
| Actinomycin D | Sigma-Aldrich | Cat#A1410 |
| N-Methyl-D-glucamine | Sigma-Aldrich | Cat#66930 |
| (+)-Sodium L-ascorbate | Sigma-Aldrich | Cat#A7631 |
| Sodium pyruvate | Sigma-Aldrich | Cat#P2256 |
| N-Acetyl-L-cysteine | Sigma-Aldrich | Cat#A7250 |
| SUPERase• In™ RNase Inhibitor | Invitrogen | AM2694 |
| Critical Commercial Assays | ||
| RNAscope Fluorescent Multiplex Reagent Kit | ACDBio | Cat#320850 |
| RNAscope HiPlex12 Ancillary Kit | ACDBio | Cat#324140 with RNAscope HiPlex Alternate Display Module (custom designed upon request, Cat# N/A) |
| Chromium Single Cell 3′ Library & Gel Bead Kit v2 | 10x Genomics | Cat# 120267 |
| Chromium i7 Multiplex Kit Kit | 10x Genomics | Cat#120262 |
| Chromium Single Cell A Chip | 10x Genomics | Cat#1000009 |
| Chromium Controller & Accessory Kit | 10x Genomics | Cat#120223 |
| Dead Cell Removal Kit | Miltenyi Biotec | Cat#130-090-101 |
| Illumina NextSeq 500 v2.5 | Illumina | Cat#20024907 |
| Single Cell-to-CT™ qRT-PCR Kit | Invitrogen | Cat#4458237 |
| Deposited Data | ||
| Mouse scRNA-seq data | Gene Expression Omnibus | GSE137478 |
| Adult zebrafish habenula scRNA-seq data from Pandey et al., 2018 | Gene Expression Omnibus | GSM2818522, GSM2818523 |
| Experimental Models: Organisms/Strains | ||
| Mouse: C57BL/6J males | The Jackson Laboratory | JAX: 000664; RRID: IMSR_JAX:000664 |
| Oligonucleotides | ||
| TaqMan® Assays-Mm-Cck | Thermo Fisher Scientific | Mm00446170_m1 |
| TaqMan® Assays-Mm-Rn18s | Thermo Fisher Scientific | Mm03928990_g1 |
| TaqMan® Assays-Mm-Spon1 | Thermo Fisher Scientific | Mm00523995_m1 |
| RNAscope® Probes, see Table S2 | ||
| Software and Algorithms | ||
| RNAscope HiPlex Image Registration Software | ACDBio | Cat#300065 |
| ImageJ (Fiji) | Schindelin et al., 2012 | RRID: SCR_002285; http://fiji.sc |
| SCENIC (v1.1.0-01) | Aibar et al., 2017 | https://aertslab.org/#scenic RRID: not found |
| R (v3.4.0 2017-04-21) | N/A | https://www.r-project.org/ RRID:SCR_001905 |
| Seurat v3 | Stuart et al., 2019 | RRID: SCR_016341; https://satijalab.org/seurat/get_started.html |
| DoubletDecon (v1.02) | DePasquale et al., 2019 |
https://github.com/EDePasquale/DoubletDecon RRID: not found |
| Enrichr | Chen et al., 2013; Kuleshov et al., 2016 |
http://amp.pharm.mssm.edu/Enrichr/ RRID:SCR_001575 |
| biomaRt | Durinck et al., 2005, 2009 |
https://bioconductor.org/packages/release/bioc/html/biomaRt.html RRID: not found |
| bioDBnet | Mudunuri et al., 2009 |
https://biodbnet-abcc.ncifcrf.gov/ RRID: not found |
| Cell Ranger | 10x Genomics | RRID: SCR_017344; https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger |
| The Gene Ontology (GO) Project | Ashburner et al., 2000 |
http://www.informatics.jax.org/mgihome/GO/project.shtml RRID:SCR_006447 |
| GraphPad Prism v8.3.0 | GraphPad Software |
https://www.graphpad.com/ RRID:SCR_002798 |
| pClamp v11.0.3 | Molecular Devices |
https://www.moleculardevices.com/ RRID:SCR_011323 |