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 |