(A) Unbiased clustering of single-nucleus RNA-sequencing (snRNA-seq) data of mouse SC cells. Each dot represents an individual cell. The cells were grouped into 26 clusters, and the cell types were …
(A) Number of genes (nGene) and number of unique molecular identifiers (nUMI) of each cluster. (B) t-Distributed stochastic neighbor embedding (t-SNE) plot of the two replicates of single-nucleus …
(A) t-Distributed stochastic neighbor embedding (t-SNE) plot displaying the distribution of excitatory neurons and inhibitor neurons from Zeisel’s study. (B) t-SNE plots showing the diversity of …
(A) Schematic diagram showing injection of AAV mixture into the superior colliculus (SC) of vGlut2-IRES-Cre mice for sparse labeling of glutamatergic SC neuron projections. (B) Two reconstructed …
(A) Schematic diagram showing current-clamp whole-cell recording from LPTN- or ZI-projecting SC neurons labeled with EGFP. (B, C) Quantitative analyses of resting membrane potential (B) and firing …
(A) Sample coronal section showing the restricted distribution of EGFP-expressing neurons in the optic nerve (Op) layer of the SC in Cbln2-IRES-Cre mice. (B) Sample micrographs showing the …
(A) Heatmap showing the computed layer specificity score of 10 differentially expressed genes (DEGs) of lateral posterior thalamic nucleus (LPTN)-projecting and zona incerta (ZI)-projecting neurons. …
Related to Figure 3D.
Related to Figure 3K.
(A, B) Sample micrographs showing the optical fiber tracks above GCaMP7-positive SC neurons in Cbln2-IRES-Cre (A) and Pitx2-Cre (B) mice. (C) Schematic diagram of the experimental configuration …
(A) Distribution of receptive field centers (red spots) of recorded Cbln2+ SC neurons in five Cbln2-IRES-Cre mice in the meridian plot of the mouse retina on the tangent screen. The coordinate …
(A) Series of schematic diagrams showing the strategy for monosynaptic retrograde tracing of Cbln2+ and Pitx2+ SC neurons using a combination of AAV and RV. Left, AAV helpers and RV used for …
(A, B) Example micrographs showing the expression of EGFP (green) and DsRed (red) in the Cbln2+ and Pitx2+ neurons in the SC of Cbln2-IRES-Cre (A) and Pitx2-Cre mice (B), respectively. Note the …
(A) Schematic diagram showing the strategy to map the efferent projections of Cbln2+ and Pitx2+ SC neurons. (B) Example coronal sections of Cbln2-IRES-Cre and Pitx2-Cre mice showing the distribution …
(A) Sample micrographs showing the distribution of EGFP-positive axons in the LPLR and LPMR (collectively the LPTN) of Cbln2-IRES-Cre (left) and Pitx2-Cre (right) mice. (B) Quantitative analysis of …
(A) Sample micrographs showing the expression of ChR2-mCherry in the Cbln2+ SC neurons of Cbln2-IRES-Cre mice (left) and the optical fiber track above the ChR2-mCherry+ axons in the LPTN (right). (B)…
(A) Schematic diagram showing whole-cell recording from ChR2-mCherry+ SC neurons in the acute brain slice. (B, C) Example traces of phase-locked spiking activity evoked by light-pulse train (1 ms, 5 …
Related to Figure 8B–C.
(A) Violin plots showing the number of detected genes (nGene) and unique molecular identifiers (uUMI) of each cell types identified in the SC. (B) Scatter plot displaying the correlation between …
(A) tSNE displaying the spatial distribution of excitatory neuron subtypes from Zeisel’s study. (B) Heatmap showing the layer specificity for each subtype computed by SPACED.
(A) Scatter plot showing the relation between number of selected genes and the number of assigned clusters. (B) Heatmap showing the computed layer specificity for each excitatory neuron subtype with …
Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
---|---|---|---|---|
Strain, strain background (Mus musculus) | Pitx2-Cre mice | Mutant Mouse Resource Center | Cat# 000126-UCD, RRID:MMRRC_000126-UCD | |
Strain, strain background (Mus musculus) | vGlut2-IRES-Cre mice | JAX Mice | Cat# JAX:028863, RRID:IMSR_JAX:028863 | |
Strain, strain background (Mus musculus) | Cbln2-IRES-Cre mice | NIBS | NA | |
Genetic reagent (virus) | AAV-EF1α-DIO-EGFP-2A-TeNT | Thomas Südhof Lab at Stanford University | NA | |
Genetic reagent (virus) | pAAV-EF1α-DIO-ChR2-mCherry | Addgene | RRID:Addgene_20297 | |
Genetic reagent (virus) | AAV-EF1α-DIO-jGCaMP7s | Addgene | RRID:Addgene_104463 | |
Genetic reagent (virus) | AAV2-retro-hSyn-DIO-EGFP | TaiTool | NA | |
Genetic reagent (virus) | AAV2/9-hSyn-DIO-EGFP-2A-TeNT | TaiTool | NA | |
Genetic reagent (virus) | AAV2/9-hSyn-DIO-EGFP | TaiTool | NA | |
Genetic reagent (virus) | AAV2/9-hSyn-DIO-ChR2-mCherry | TaiTool | NA | |
Genetic reagent (virus) | AAV2/9-hSyn-DIO-mCherry | TaiTool | NA | |
Genetic reagent (virus) | AAV2/9-hSyn-DIO-jGCaMP7s | TaiTool | NA | |
Genetic reagent (virus) | AAV2/9-EF1α-DIO-EGFP-2A-TVA | BrainVTA | NA | |
Genetic reagent (virus) | AAV2/9-EF1α-DIO-RV-G | BrainVTA | NA | |
Genetic reagent (virus) | RV-EnvA-ΔG-DsRed | BrainVTA | NA | |
Antibody | Rabbit polyclonal anti-EGFP | Abcam | Cat# ab290, RRID:AB_303395 | |
Antibody | Polycolonal anti-mCherry | Abcam | Cat# ab167453, RRID:AB_2571870; Cat# ab205402, RRID:AB_2722769 | |
Sequence-based reagent | M-Cbln2-cre-upF | Tsingke Biological Technology, China | Primer | 5’-GGTACCTACTGTGTATCGCCAG-3’ |
Sequence-based reagent | CRE-AS | Tsingke Biological Technology, China | Primer | 5’-CTGTTTCACTATCCAGGTTACG-3’ |
Sequence-based reagent | CRE-S | Tsingke Biological Technology, China | Primer | 5’-TACTGACGGTGGGAGAATG-3’ |
Sequence-based reagent | M-Cbln2-ires-cre-doR | Tsingke Biological Technology, China | Primer | 5’-GTTTGAAGCTGCACTGAGAGAG-3’ |
Chemical compound, drug | D-AP5/CNQX | Tocris | Cat# 0106 / 0190 | |
Chemical compound, drug | Picrotoxin/TTX | Tocris | Cat# 1128 / 1078 | |
Chemical compound, drug | 4-AP | Sigma | Cat# 275875 | |
Chemical compound, drug | DAPI | Sigma | Cat# D8417 | |
Software, algorithm | GraphPad Prism 9.0.0 | GraphPad, 2015 | https://www.graphpad.com/scientific-software/prism/ | |
Software, algorithm | Cell ranger 3.0.2 | Zheng et al., 2017 | http://10xgenomics.com | |
Software, algorithm | R version 3.6.1 | R Development Core Team, 2020 | https://www.r-project.org | |
Software, algorithm | Seurat 3.1.0 | Stuart et al., 2019 | https://satijalab.org/seurat/ | |
Software, algorithm | Scrublet 0.2.1 | Wolock et al., 2019 | https://github.com/swolock/scrublet | |
Software, algorithm | batchelor 1.0.1 | Haghverdi et al., 2018 | https://github.com/MarioniLab/MNN2017/ | |
Software, algorithm | pheatmap 1.0.12 | Kolde, 2019 | https://github.com/raivokolde/pheatmap | |
Software, algorithm | rgl 0.100.54 | Adler and Murdoch, 2020 | https://github.com/dmurdoch/rgl | |
Software, algorithm | metascape | Zhou et al., 2019 | https://metascape.org/gp/index.html#/main/step1 | |
Software, algorithm | Image J v1.48h3 | Schneider et al., 2012 | https://imagej.nih.gov/ij/ | |
Software, algorithm | MATLAB 2019b | MATLAB, 2018 | https://www.mathworks.com | |
Software, algorithm | Brainrender 2.0 | Claudi et al., 2020 | https://github.com/brainglobe/brainrender |
Sample information for high-throughput single-nucleus RNA-sequencing (snRNA-seq) of nucleus from superior colliculus (SC) and top 50 differentially expressed genes among nine major cell types in SC, related to Figure 1A.
Differentially expressed genes among 9 excitatory neuron subtypes and 10 inhibitory neuron subtypes, related to Figure 1C–D.
Sample information for patch-seq of neurons from superior colliculus (SC), related to Figure 2H.
Differentially expressed genes between zona incerta (ZI)- and lateral posterior thalamic nucleus (LPTN)-projecting neurons in superior colliculus (SC), related to Figure 2I.
Differentially expressed genes between excitatory neuron subtype Ex-3 and Ex-6, and between Ex-1 and Ex-4, related to Figure 2L–M, respectively.
Summary of all experimental designs.
Summary of cell-counting strategies.
Summary of statistical analyses.