KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Bacterial and Virus Strains | ||
| rAAV2-retro-EF1a-Cre | Tervo et al., 2016; Allen Institute Viral Core | N/A |
| rAAV2-retro-CAG-GFP | Tervo et al., 2016 | N/A |
| rAAV2-retro-CAG-tdTomato | Tervo et al., 2016 | N/A |
| rAAV2-retro-EF1a-dTomato | Tervo et al., 2016; Allen Institute Viral Core | N/A |
| RVΔGL-Cre | Chatterjee et al., 2018; from the lab of Ian Wickersham | N/A |
| CAV-Cre | Hnasko et al., 2006; from the lab of Miguel Chillon Rodrigues | N/A |
| rAAV-mscRE4-minBGpromoter-FlpO-WPRE3 | Graybuck et al., 2021; Allen Institute Viral Core | N/A |
| rAAV-mscRE10-minBGpromoter-FlpO-WPRE3 | Graybuck et al., 2021; Allen Institute Viral Core | N/A |
| rAAV-mscRE16-minBGpromoter-FlpO-WPRE3 | Graybuck et al., 2021; Allen Institute Viral Core | N/A |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Trimethoprim (TMP) | Sigma-Aldrich | T7883-5G |
| Tamoxifen (TAM) | Sigma-Aldrich | T5648-5G |
| Critical Commercial Assays | ||
| SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing | Takara | 634894 |
| Nextera XT Index Kit V2 Set A-D | Illumina | FC-131-2001, FC-131-2002, FC-131-2003, FC-131-2004 |
| Chromium Single Cell 3’ Reagent Kit v2 | 10x Genomics | 120237 |
| Deposited Data | ||
| Transcriptomic data – fastq files | This paper; NeMO | https://assets.nemoarchive.org/dat-jb2f34y |
| Transcriptomic data – SMART-seq processed count file and sample metadata | This paper; Allen Institute for Brain Science; NeMO | https://portal.brain-map.org/atlases-and-data/rnaseq/mouse-whole-cortex-and-hippocampus-smart-seq; https://assets.nemoarchive.org/dat-jb2f34y |
| Transcriptomic data – 10x processed count file and sample metadata | This paper; Allen Institute for Brain Science; NeMO | https://portal.brain-map.org/atlases-and-data/rnaseq/mouse-whole-cortex-and-hippocampus-10x; https://assets.nemoarchive.org/dat-jb2f34y |
| Cell type cards website that provides specific information for each cell type: markers, cell type metadata, correspondence with cell types in previous publications and relation to neighboring cell types | This paper; Allen Institute for Brain Science | https://taxonomy.shinyapps.io/ctx_hip_browser_v2/ |
| Experimental Models: Organisms/Strains | ||
| Mouse: B6.Cg-Gt(ROSA)26Sortm14(CAG-tdTomato)Hze/J, Ai14(RCL-tdT) | The Jackson Laboratory | RRID: IMSR_JAX:007914 |
| Mouse: B6;129S-Gt(ROSA)26Sortm65.1(CAG-tdTomato)Hze/J, Ai65(RCFL-tdT) | The Jackson Laboratory | RRID: IMSR_JAX:021875 |
| Mouse: B6;129S-Gt(ROSA)26Sortm66.1(CAG-tdTomato)Hze/J, Ai66(RCRL-tdT) | The Jackson Laboratory | RRID: IMSR_JAX:021876 |
| Mouse: Ai65F(RCF-tdT) | Daigle et al., 2018 | N/A |
| Mouse: Ai110(RCL-FnGF-nT) | Daigle et al., 2018 | N/A |
| Mouse: B6.Cg-Gt(ROSA)26Sortm75.1(CAG-tdTomato*)Hze/J, Ai75(RCL-nT) | The Jackson Laboratory | RRID: IMSR_JAX:025106 |
| Mouse: B6.Cg-Igs7tm140.1(tetO-EGFP,CAG-tTA2)Hze/J, Ai140(TIT2L-GFP-ICL-tTA2) | The Jackson Laboratory | RRID: IMSR_JAX:030220 |
| Mouse: B6.Cg-Igs7tm148.1(tetO-GCaMP6f,CAG-tTA2)Hze/J, Ai148(TIT2L-GC6f-ICL-tTA2) | The Jackson Laboratory | RRID: IMSR_JAX:030328 |
| Mouse: B6.Cg-Snap25tm1.1Hze/J, Snap25-LSL-F2A-GFP | The Jackson Laboratory | RRID: IMSR_JAX:021879 |
| Mouse: B6.Cg-Calb1tm2.1(cre)Hze/J, Calb1-IRES2-Cre | The Jackson Laboratory | RRID: IMSR_JAX:028532 |
| Mouse: B6(Cg)-Calb2tm1(cre)Zjh/J, Calb2-IRES-Cre | The Jackson Laboratory | RRID: IMSR_JAX:010774 |
| Mouse: STOCK Ccktm1.1(cre)Zjh/J, Cck-IRES-Cre | The Jackson Laboratory | RRID: IMSR_JAX:012706 |
| Mouse: B6;129S6-Chattm2(cre)Lowl/J, Chat-IRES-Cre | The Jackson Laboratory | RRID: IMSR_JAX:006410 |
| Mouse: STOCK Tg(Chrna2-cre)OE25Gsat/Mmucd, Chrna2-Cre_OE25 | MMRRC | RRID: MMRRC_036502-UCD |
| Mouse: STOCK Tg(Chrnb3-cre)SM93Gsat/Mmucd, Chrnb3-Cre_SM93 | MMRRC | RRID: MMRRC_036469-UCD |
| Mouse: B6(Cg)-Crhtm1(cre)Zjh/J, Crh-IRES-Cre_ZJH | The Jackson Laboratory | RRID: IMSR_JAX:012704 |
| Mouse: B6.Cg-Ccn2tm1.1(folA/cre)Hze/J, Ctgf-T2A-dgCre | The Jackson Laboratory | RRID: IMSR_JAX:028535 |
| Mouse: B6(Cg)-Cux2tm3.1(cre/ERT2)Mull/Mmmh, Cux2-CreERT2 | MMRRC | RRID: MMRRC_032779-MU |
| Mouse: B6;129S-Esr2tm1.1(cre)Hze/J, Esr2-IRES2-Cre | The Jackson Laboratory | RRID: IMSR_JAX:030158 |
| Mouse: B6(Cg)-Etv1tm1.1(cre/ERT2)Zjh/J, Etv1-CreERT2 | The Jackson Laboratory | RRID: IMSR_JAX:013048 |
| Mouse: B6J.Cg-Gad2tm2(cre)Zjh/MwarJ, Gad2-IRES-Cre | The Jackson Laboratory | RRID: IMSR_JAX:028867 |
| Mouse: STOCK Tg(Colgalt2-cre)NF107Gsat/Mmucd, Glt25d2-Cre_NF107 | MMRRC | RRID: MMRRC_036504-UCD |
| Mouse: B6.Cg-Gnb4tm1.1(cre/ERT2)Hze/J, Gnb4-IRES2-CreERT2 | The Jackson Laboratory | RRID: IMSR_JAX:030159 |
| Mouse: Tg(Gng7-cre)KH71Gsat, Gng7-Cre_KH71 | Gerfen et al., 2013; from the lab of Charles Gerfen | MGI:4367014 |
| Mouse: STOCK Tg(Htr3a-cre)NO152Gsat/Mmucd, Htr3a-Cre_NO152 | MMRRC | RRID: MMRRC_036680-UCD |
| Mouse: B6.Cg-Ndnftm1.1(folA/cre)Hze/J, Ndnf-IRES2-dgCre | The Jackson Laboratory | RRID: IMSR_JAX:028536 |
| Mouse: STOCK Nkx2-1tm1.1(cre/ERT2)Zjh/J, Nkx2.1-CreERT2 | The Jackson Laboratory | RRID: IMSR_JAX:014552 |
| Mouse: B6;129S-Nos1tm1.1(cre/ERT2)Zjh/J, Nos1-CreERT2 | The Jackson Laboratory | RRID: IMSR_JAX:014541 |
| Mouse: B6;129S-Npr3tm1.1(cre)Hze/J, Npr3-IRES2-Cre | The Jackson Laboratory | RRID: IMSR_JAX:031333 |
| Mouse: B6.Cg-Npytm1.1(flpo)Hze/J, Npy-IRES2-FlpO | The Jackson Laboratory | RRID: IMSR_JAX:030211 |
| Mouse: FVB-Tg(Nr5a1-cre)2Lowl/J, Nr5a1-Cre | The Jackson Laboratory | RRID: IMSR_JAX:006364 |
| Mouse: B6.FVB(Cg)-Tg(Ntsr1-cre)GN220Gsat/Mmucd, Ntsr1-Cre_GN220 | MMRRC | RRID: MMRRC_030648-UCD |
| Mouse: B6;129S-Oxtrtm1.1(cre)Hze/J, Oxtr-T2A-Cre | The Jackson Laboratory | RRID: IMSR_JAX:031303 |
| Mouse: B6;129S-Pdyntm1.1(cre/ERT2)Hze/J, Pdyn-T2A-CreERT2 | The Jackson Laboratory | RRID: IMSR_JAX:030197 |
| Mouse: B6;129S-Penktm2(cre)Hze/J, Penk-IRES2-Cre-neo | The Jackson Laboratory | RRID: IMSR_JAX:025112 |
| Mouse: B6.Cg-Pvalbtm3.1(dreo)Hze/J, Pvalb-T2A-Dre | The Jackson Laboratory | RRID: IMSR_JAX:021190 |
| Mouse: B6.Cg-Pvalbtm4.1(flpo)Hze/J, Pvalb-T2A-FlpO | The Jackson Laboratory | RRID: IMSR_JAX:022730 |
| Mouse: B6;129P2-Pvalbtm1(cre)Arbr/J, Pvalb-IRES-Cre | The Jackson Laboratory | RRID: IMSR_JAX:008069 |
| Mouse: B6.Cg-Rasgrf2tm2.1(folA/flpo)Hze/J, Rasgrf2-T2A-dgFlpO | The Jackson Laboratory | RRID: IMSR_JAX:029589 |
| Mouse: STOCK Tg(Rbp4-cre)KL100Gsat/Mmucd, Rbp4-Cre_KL100 | MMRRC | RRID: MMRRC_031125-UCD |
| Mouse: B6;129S-Rorbtm1.1(cre)Hze/J, Rorb-IRES2-Cre | The Jackson Laboratory | RRID: IMSR_JAX:023526 |
| Mouse: B6.Cg-Rorbtm3.1(flpo)Hze/J, Rorb-IRES2-FlpO | The Jackson Laboratory | RRID: IMSR_JAX:029590 |
| Mouse: Rorb-P2A-FlpO | Daigle et al., 2018 | N/A |
| Mouse: B6;C3-Tg(Scnn1a-cre)2Aibs/J, Scnn1a-Tg2-Cre | The Jackson Laboratory | RRID: IMSR_JAX:009112 |
| Mouse: B6;C3-Tg(Scnn1a-cre)3Aibs/J, Scnn1a-Tg3-Cre | The Jackson Laboratory | RRID: IMSR_JAX:009613 |
| Mouse: STOCK Tg(Sim1-cre)KJ18Gsat/Mmucd, Sim1-Cre_KJ18 | MMRRC | RRID: MMRRC_031742-UCD |
| Mouse: B6J.129S6(FVB)-Slc17a6tm2(cre)Lowl/MwarJ, Slc17a6-IRES-Cre | The Jackson Laboratory | RRID: IMSR_JAX:028863 |
| Mouse: B6;129S-Slc17a7tm1.1(cre)Hze/J, Slc17a7-IRES2-Cre | The Jackson Laboratory | RRID: IMSR_JAX:023527 |
| Mouse: STOCK Tg(Slc17a8-icre)1Edw/SealJ, Slc17a8-iCre | The Jackson Laboratory | RRID: IMSR_JAX:018147 |
| Mouse: B6;129S-Slc17a8tm1.1(cre)Hze/J, Slc17a8-IRES2-Cre | The Jackson Laboratory | RRID: IMSR_JAX:028534 |
| Mouse: B6J.129S6(FVB)-Slc32a1tm2(cre)Lowl/MwarJ, Slc32a1-IRES-Cre | The Jackson Laboratory | RRID: IMSR_JAX:028862 |
| Mouse: B6.Cg-Slc32a1tm1.1(flpo)Hze/J, Slc32a1-IRES2-FlpO | The Jackson Laboratory | RRID: IMSR_JAX:031331 |
| Mouse: B6.Cg-Slc32a1tm1.1(flpo)Hze/J, Slc32a1-T2A-FlpO | The Jackson Laboratory | RRID: IMSR_JAX:029591 |
| Mouse: B6;129S-Snap25tm2.1(cre)Hze/J, Snap25-IRES2-Cre | The Jackson Laboratory | RRID: IMSR_JAX:023525 |
| Mouse: B6J.Cg-Ssttm2.1(cre)Zjh/MwarJ, Sst-IRES-Cre | The Jackson Laboratory | RRID: IMSR_JAX:028864 |
| Mouse: B6J.Cg-Ssttm3.1(flpo)Zjh/AreckJ, Sst-IRES-FlpO | The Jackson Laboratory | RRID: IMSR_JAX:031629 |
| Mouse: B6;129S-Tac1tm1.1(cre)Hze/J, Tac1-IRES2-Cre | The Jackson Laboratory | RRID: IMSR_JAX:021877 |
| Mouse: B6.FVB(Cg)-Tg(Th-cre)FI172Gsat/Mmucd, Th-Cre_FI172 | MMRRC | RRID: MMRRC_031029-UCD |
| Mouse: C57BL/6N-Thtm1Awar/Mmmh, Th-P2A-FlpO or TH-2A-Flpo | Poulin et al., 2018; MMRRC | RRID: MMRRC_050618-MU |
| Mouse: B6.FVB(Cg)-Tg(Tlx3-cre)PL56Gsat/Mmucd, Tlx3-Cre_PL56 | MMRRC | RRID: MMRRC_041158-UCD |
| Mouse: B6.Cg-Trib2tm1.1(cre/ERT2)Hze/J, Trib2-F2A-CreERT2 | The Jackson Laboratory | RRID: IMSR_JAX:022865 |
| Mouse: B6J.Cg-Viptm1(cre)Zjh/AreckJ, Vip-IRES-Cre | The Jackson Laboratory | RRID: IMSR_JAX:031628 |
| Mouse: STOCK Viptm2.1(flpo)Zjh/J, Vip-IRES-FlpO | The Jackson Laboratory | RRID: IMSR_JAX:028578 |
| Mouse: B6;129S-Vipr2tm1.1(cre)Hze/J, Vipr2-IRES2-Cre | The Jackson Laboratory | RRID: IMSR_JAX:031332 |
| Mouse: STOCK Tg(Gad1-EGFP)98Agmo/J, Gad67-GFP_X98 | The Jackson Laboratory | RRID: IMSR_JAX:006340 |
| Software and Algorithms | ||
| STAR 2.5.3 | Dobin et al., 2013 | https://github.com/alexdobin/STAR/releases |
| CellRanger | 10x Genomics | https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest |
| SpaceRanger | 10x Genomics | https://support.10xgenomics.com/spatial-gene-expression/software/downloads/latest |
| scrattch suites for clustering/visualization of single cell dataset that include scrattch.vis, scrattch.hicat, scrattch.bigcat | This paper; Allen Institute for Brain Science | https://github.com/AllenInstitute/scrattch; https://github.com/AllenInstitute/scrattch.vis; https://github.com/AllenInstitute/scrattch.hicat; https://github.com/AllenInstitute/scrattch.bigcat |
| Seurat v3.4 | Stuart et al., 2019 | https://github.com/satijalab/seurat |
| UMAP | McInnes et al., 2018 | https://github.com/lmcinnes/umap |
| R v3.5.0 and greater | R Foundation | https://www.R-project.org |
| RStudio IDE | RStudio | http://www.rstudio.com |