KEY RESOURCES TABLE.
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
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| Antibodies | ||
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| Polyclonal rabbit anti-DsRed | Clontech | Cat #632496; RRID:AB_10013483 |
| Polyclonal goat anti-GFP | Sicgen | Cat# AB0020-200; RRID:AB_2333099 |
| Rat anti-RFP | Chromotek | #5f8; RRID:AB_2336064 |
| Rabbit anti-somatostatin | Peninsula Laboratories | T4103; RRID:AB_518614 |
| Mouse anti-Calretinin | Millipore | Cat# MAB1568; RRID:AB_94259 |
| Rabbit anti-Calretinin | Swant | Cat# CR 7697; RRID:AB_2619710 |
| Rabbit anti-Satb2 | Abcam | Cat# ab34735; RRID:AB_2301417 |
| Mouse IgG1 anti-Gephyrin | Synaptic Systems | Cat# 147 011; RRID:AB_2810215 |
| Polyclonal chicken anti-GFP | Aves Labs | Cat# 1020; RRID:AB_10000240 |
| Mouse IgG2a anti-Gad65 | Millipore | Cat# MAB351R; RRID:AB_94905 |
| Alexa Fluor™ 488, Donkey anti-Goat | Thermo Fisher Scientific | Cat# A-11055, RRID:AB_2534102 |
| Alexa Fluor™ 594, Donkey anti-Rabbit | Thermo Fisher Scientific | Cat# A-21207, RRID:AB_141637 |
| Alexa Fluor™ 594, Donkey anti-Rat | Thermo Fisher Scientific | Cat# A-21209, RRID:AB_2535795 |
| Alexa Fluor™ 647, Donkey anti-Rabbit | Thermo Fisher Scientific | Cat# A-31573, RRID:AB_2536183 |
| Alexa Fluor™ 647, Goat anti-Mouse IgG1 | Thermo Fisher Scientific | Cat# A-21240, RRID:AB_2535809 |
| Alexa Fluor® 488 polyclonal Donkey anti-Chicken | Jackson ImmunoResearch Labs | Cat# 703-545-155, RRID:AB_2340375 |
| DyLightTM 405 Polyclonal Goat anti-Mouse IgG2a | Jackson ImmunoResearch Labs | Cat# 115-477-186, RRID:AB_2632530 |
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| Bacterial and virus strains | ||
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| rAAV9-hSyn-DIO-TVA-GFP-N2cG | This paper | RRID:Addgene_175439 |
| rAAV1/2-Dlx-DIO-TVA | This paper | N/A |
| rAAV1/2-Dlx-DIO-GFP-N2cG | This paper | N/A |
| rAAV9-Dlx-DIO-TVA | This paper | N/A |
| rAAV9-Dlx-DIO-GFP-N2cG | This paper | N/A |
| rAAV2-retro-hSyn-mScarlet | Dr. David Ginty This paper | N/A |
| rAAV PHP.eB-S5E2-GFP-fGFP | This paper | RRID:Addgene_135631 |
| rAAV9-hDlx-Flex-dTomato | This paper | RRID:Addgene_83894 |
| EnvA-CVS-N2C(DG)-FlpO-mCherry | K. Ritola, Janelia Pouchelon et al.37 PMID: 34758329 PMCID: PMC8832360 |
N/A |
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| Chemicals, peptides, and recombinant proteins | ||
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| Tamoxifen | Sigma-Aldrich | Cat# T5648 |
| Corn Oil | Sigma-Aldrich | Cat# C8267 |
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| Critical commercial assays | ||
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| RNAscope® Multiplex Fluorescent Reagent Kit v2 Assay | Advanced Cell Diagnostics | Cat. No. 323100 |
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| Deposited data | ||
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| P28 cortical interneuron snRNA-seq data | Allaway et al.22 PMID: 34552240 PMCID: PMC9316417 |
GEO: GSE165233 |
| Mouse Whole Cortex and Hippocampus Smart-Seq | Yao et al.3 PMID: 34004146 PMCID: PMC8195859 |
GEO: GSE185862 |
| Slide-SeqV2 data | This paper | https://singlecell.broadinstitute.org/single_cell/study/SCP2082/cortical-somatostatin-interneuron-subtypes-form-cell-type-specific-circuits#study-summary |
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| Experimental models: Organisms/strains | ||
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| Mouse: C57BL/6J | Jackson Laboratories | RRID:IMSR_JAX:000664 |
| Mouse: B6 Ssttm2.1(cre)Zjh/J | Jackson Laboratories | RRID:IMSR_JAX:013044 |
| Mouse: B6J.Cg-Ssttm3.1(flpo)Zjh/AreckJ | Jackson Laboratories | RRID:IMSR_JAX:031629 |
| Mouse: B6;129S-Tac1tm1.1(cre)Hze/J | Jackson Laboratories | RRID:IMSR_JAX:021877 |
| Mouse: B6(Cg)-Etv1tm1.1(cre/ERT2)ZJh/J | Jackson Laboratories | RRID:IMSR_JAX:013048 |
| Mouse: B6;129S-Pdyntm1.1(cre)Mjkr/LowlJ | Jackson Laboratories | RRID:IMSR_JAX:027958 |
| Mouse: B6;129S-Pdyntm1.1(cre/ERT2)Hze/J | Jackson Laboratories | RRID:IMSR_JAX:030197 |
| Mouse: B6.Cg-Npytm1.1(flpo)Hze/J | Jackson Laboratories | RRID:IMSR_JAX:030211 |
| Mouse: B6.Cg-Hpseem1(cre)Ngai/TasicJ | Dr. David A. Stafford | RRID:IMSR_JAX:037334 |
| Mouse: Chrna2-Cre (Tg(Chrna2-cre)1Kldr) | Dr. Klas KullanderHilscher et al.30 PMID: 28182735 PMCID: PMC5300109 |
N/A |
| Mouse: CrhCre | Dr. Bradford Lowell Krashes et al.52 PMID: 24487620 PMCID: PMC3955843 |
N/A |
| Mouse: B6.129S4(SJL)-Crhr2tm1.1(cre)Lbrl/J | Jackson Laboratories | RRID:IMSR_JAX:033728 |
| Mouse: B6.Cg-Gt(ROSA) 26Sortm65.2(CAG-tdTomato)Hze/J; Ai65 | Jackson Laboratories | RRID:IMSR_JAX:021875 |
| Mouse: B6.Cg-Gt(ROSA) 26Sortm14(CAG-tdTomato)Hze/J; Ai14 | Jackson Laboratories | RRID:IMSR_JAX:007914 |
| Mouse: B6.Cg-Gt(ROSA) 26Sortm9(CAG-tdTomato)Hze/J; Ai9 | Jackson Laboratories | RRID:IMSR_JAX:007909 |
| Mouse: B6;129S4-Gt(ROSA) 26Sortm3(CAG-tdTomato,-EGFP*)Zjh/J; IS reporter | Jackson Laboratories | RRID:IMSR_JAX:028582 |
| Mouse: B6.Cg-Gt(ROSA) 26Sortm32(CAG-COP4*H134R/EYFP)Hze/J; Ai32 | Jackson Laboratories | RRID:IMSR_JAX:024109 |
| Mouse: B6.Cg-Gt(ROSA) 26Sortm80.1(CAG-COP4*L132C/EYFP)Hze/J; Ai80 | Jackson Laboratories | RRID:IMSR_JAX:025109 |
| Mouse: B6;129S6-Gt(ROSA) 26Sortm10(CAG-Syp/EGFP*,-tdTomato)Dym/J; RC::FPSit | Jackson Laboratories | RRID:IMSR_JAX:030206 |
| Mouse: Gt(ROSA)26Sortm1.1(CAG-EGFP)Fsh/Mmjax; RCE:loxP | MMRRC | RRID:MMRRC_032037-JAX |
| Mouse: Gt(ROSA)26Sortm1.2(CAG-EGFP)Fsh/Mmjax; RCE:FRT | MMRRC | RRID:MMRRC_032038-JAX |
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| Oligonucleotides | ||
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| RNAscope® Probe- Mm-Gad1 | ACDBio | Cat#400951 |
| RNAscope® Probe- Mm-Sst | ACDBio | Cat#404631, 404631-C2, 404631-C3, 404631-C4 |
| RNAscope® Probe- Mm-Calb2 | ACDBio | Cat#313641-C3 |
| RNAscope® Probe- Mm-Hpse | ACDBio | Cat#412251 |
| RNAscope® Probe- Mm-Cbln4 | ACDBio | Cat#428471 |
| RNAscope® Probe- Mm-Pdyn | ACDBio | Cat#318771 |
| RNAscope® Probe- Mm-Crh | ACDBio | Cat#316091-C2 |
| RNAscope® Probe- Mm-Chodl | ACDBio | Cat#450211 |
| RNAscope® Probe- tdTomato | ACDBio | Cat#317041-C2 |
| HCR RNA-FISH probe Sst - B5 | Molecular Instruments | N/A |
| HCR RNA-FISH amplifier B5 - Alexa Fluor 647 | Molecular Instruments | N/A |
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| Software and algorithms | ||
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| Code for snRNA-seq and Slide-SeqV2 analysis | This paper | https://github.com/gs512/slideseq-engine |
| Zen blue 2.6 | Zeiss | RRID:SCR_013672 |
| ImageJ | NIH | RRID:SCR_003070 |
| Fiji | http://fiji.sc | RRID:SCR_002285 |
| Adobe Photoshop CS6 | Adobe | RRID:SCR_014199 |
| Adobe Illustrator CS6 | Adobe | RRID:SCR_014198 |
| R Project for Statistical Computing | Open Source | RRID:SCR_001905 |
| RStudio | Open Source | RRID:SCR_000432 |
| Seurat | Rahul Satija Lab | https://satijalab.org/seurat/ |
| SPACEXR (formerlly RCTD) | Fei Chen Lab | https://github.com/dmcable/spacexr |
| ClampFit 11 | Molecular Devices | RRID:SCR_011323 |
| Neurolucida 360 | MBF Bioscience | RRID:SCR_016788 |
| NeuroInfo® | MBF Bioscience | https://www.mbfbioscience.com/neuroinfo |
| Prism 9.1.2 | Graphpad Software | RRID:SCR_002798 |
| IBM SPSS Statistics 26 | IBM | RRID:SCR_019096 |
| MATLAB | MathWorks | https://www.mathworks.com/ |