KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Goat polyclonal anti-c-fos | Santa Cruz Biotechnology | Cat# sc-52-g; RRID: AB_2629503 |
| Donkey anti-goat, Alexa Fluor 647 | Invitrogen | Cat# A-21447; RRID: AB_2535864 |
| Bacterial and Virus Strains | ||
| rAAV2-retro-EF1a-Cre | Tervo et al., 2016 | N/A |
| HSV1-LS1L-EYFP | MGH Vector Core | N/A |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Pronase | Sigma | Cat# P6911-1G |
| Papain | Sigma | Cat# P3125-250MG |
| Egg White/BSA ovomucoid inhibitor | Worthington | Cat# OI-BSA |
| DNase I | Thermo scientific | Cat# 90083 |
| DNase/RNase-Free Distilled Water | Thermo scientific | Cat# 10977-015 |
| 10X PBS | Thermo scientific | Cat# AM9624 |
| DAPI | Sigma | Cat# D9542-10MG |
| BSA | Thermo scientific | Cat# AM2616 |
| Actinomycin D | Sigma | Cat# A1410-2MG |
| Kynurenic acid sodium salt | Abcam | Cat# ab120256 |
| L-Cysteine | Sigma | Cat# W326305-100G |
| D-(+)-Trehalose dihydrate | Sigma | Cat# 90210-50G |
| Ethylenediaminetetraacetic acid | Sigma | Cat# 03690-100ML |
| MgSO4solution | Sigma | Cat# 83266-100ML-F |
| CaCl2solution | Sigma | Cat# 21115-100ML |
| Sodium nitrite | Sigma | Cat# 237213-100G |
| Heparin sodium salt | Sigma | Cat# H4784-250MG |
| Paraformaldehyde | EMS | Cat# 15714-S |
| Sucrose, RNase & DNase Free | Amresco | Cat# 0335-2.5KG |
| Critical Commercial Assays | ||
| SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing | Takara | Cat# 634894 |
| Nextera XT Index Kit V2 Set A | Illumina | FC-131-2001 |
| Nextera XT DNA Library Preparation | Illumina | FC-131-1096 |
| Chromium Single Cell 3′ Library & Gel Bead Kit v2 | 10x Genomics | PN-120237 |
| Chromium Single Cell 3′ Chip Kit v2 | 10x Genomics | PN-120236 |
| Chromium i7 Multiplex Kit | 10x Genomics | PN-120262 |
| Experimental Models: Organisms/Strains | ||
| Mouse: Nr5a1-Cre | Dhillon et al., 2006 | N/A |
| Mouse: Oxtr-T2A-Cre | Daigle et al., 2018 | N/A |
| Mouse: Vglut2-ires-cre | The Jackson Laboratory | JAX: 016963 |
| Mouse: Esr1-Cre | Lee et al., 2014 | N/A |
| Mouse: Ai14(RCL-tdTomato) | Madisen et al., 2010 | N/A |
| Mouse: Ai110(RCL-FnGF-nT) | Daigle et al., 2018 | N/A |
| Mouse: C57BL/6N | Charles River | N/A |
| Mouse: BALB/c | Charles River | N/A |
| Software and Algorithms | ||
| CellRanger v3.0.2 | 10x Genomics | http://www.10xgenomics.com/ |
| MATLAB Version 2017a | MathWorks | https://www.mathworks.com |
| R v.3.3.0 | R Foundation | https://www.r-project.org |
| Seurat v3.0.3 | Butler et al., 2018; Stuart et al., 2019 | https://satijalab.org/seurat/ |
| scrattch.hicat | Tasic et al., 2018 | https://github.com/AllenInstitute/scrattch.hicat |
| seqFISH image processing code (MATLAB) | Shah et al., 2016; Eng et al., 2019 | N/A |
| SMART-seq, 10x, and seqFISH data analysis code code (MATLAB and R) | This paper | N/A |
| Prism 6 | GraphPad Software | https://www.graphpad.com/ |
| ImageJ | NIH | https://imagej.nih.gov/ij |