Molecular, cellular, and developmental organization of the mouse vomeronasal organ at single cell resolution
- Stowers Institute for Medical Research, United States
- Department of Cell Biology and Physiology, University of Kansas Medical Center, United States
Figures
Figure 1 with 3 supplements
Single cell transcriptomic profile of the whole vomeronasal organ.
UMAP visualization of integrated cell-type clusters for whole-VNO single-cell RNA-seq. (B) Cell-type marker-gene normalized expression across the cell clusters. C. UMAP of cell-type clusters split …
Figure 1—figure supplement 1
Age differences in gene expression.
(A) Volcano plot of gene expression differences between P14 and P56 (Wilcoxon rank sum test, FDR ≤ 0.05). (B) 16 significantly differentially expressed genes with largest positive or negative …
Figure 1—figure supplement 2
Sex differences in gene expression.
(A) Volcano plot of gene expression differences between male and female mice (Wilcoxon rank sum test, FDR ≤ 0.05). (B) 16 significantly differentially expressed chemosensory receptors with largest …
Figure 1—figure supplement 3
Zonal distribution of cell types in the VNO neuroepithelia.
(A) Schematic indicating quantification of cells in the marginal, intermediate, and main zones. (B) Stacked bar-plot of cell-type proportions by VNO zone (Wilcoxon rank sum test, FDR ≤ 0.05). (C) …
Figure 2 with 3 supplements
Novel neuronal lineage.
(A) UMAP visualization of cell-type clusters for the neuronal lineage. (B) Expression of Gnai2 and Gnao1 in the neuronal lineage. (C) Expression of Cnga2 and Gnal in the OSN lineage. (D–E) Location …
Figure 2—figure supplement 1
Neuronal lineage features and differentially expressed genes in sVSNs.
(A and B) Normalized Gap43 and Stmn2 expression in the neuronal lineage. (C) Normalized. Xist expression in the neuronal lineage, split by sex. (D) Violin plot of normalized Gnai2. expression in …
Figure 2—figure supplement 2
Significantly regulated genes in sVSNs.
(A-D) Feature plots showing odor binding protein gene expression (Muc2, Obp2a, Obp2b, and Lcn3). (E–L) Top upregulated genes in sVSNs. (M–T) Top downregulated genes in sVSNs.
Figure 2—figure supplement 3
sVSN Pseudotime, OSN markers and GO Terms.
(A) VNO neuronal lineage cell-types in UMAP space. (B) V1R, V2R, and sVSN lineage. pseudotimes in UMAP space. (C) Volcano plot of mOSN gene expression versus all other cells. from the neuronal …
Figure 3 with 1 supplement
Molecular cascades separating the neuronal lineages.
(A) PCA plot of V1R and V2R pseudotime principal curves across cell types. (B) Cell density plots across pseudotime for P14 and P56 mice (Two-sided Kolmogorov-Smirnov test). (C) Heatmap showing …
Figure 3—figure supplement 1
Genes expressed during INP to immature neuron transition.
(A and B) Violin plot of normalized expression for Neurog1 (A) and Neurod1 (B) split by cell type. (C–R) Feature plots of normalized gene expression for early differentially expressed genes between …
Figure 4 with 2 supplements
Receptor expression in the VNO.
(A-D) Expression level of individual receptor (total raw counts) plot against the number of cells expressing the receptor for V1R (A), V2R (B), VNO-Olfr (C), and MOE-Olfr (D). (E-H) Ranked …
Figure 4—figure supplement 1
Receptor distribution in the VNO.
(A) Log scale rank-frequency distribution plots for V1R, V2R, VSN-OR, and OSN-OR. (B–D) Number of cells expressing (nCells) vs. total raw counts for V1R, V2R, and VSN-OR. (E–F). Rank by average …
Figure 4—figure supplement 2
Co-expression between vomeronasal receptors and transcription factors.
(A) Distribution density plot showing relationship between similarity of transcription factor (TF) gene expression profiles and receptor sequence similarity. (B–C) Heatmaps showing the. V1R-TF (B) …
Figure 5 with 1 supplement
Co-expression among VNO receptor classes.
(A) Shannon Indices showing the specificity of receptor expression. High values indicate more co-expressions. (B–C) Prevalence and level of receptor co-expression by age and cell- type for the V1R (B…
Figure 5—figure supplement 1
Receptor expression statistics.
(A-C) Percent of all read counts from a receptor gene (A), number of receptor species present. per cell (B), and total counts from vomeronasal receptors (C), separated by cell type (Wilcoxon rank …
Figure 6
Axon guidance molecules associated with receptor genes.
(A) Distribution density plot showing relationship between similarity of axon guidance (AG) gene expression profiles and receptor sequence similarity. The distribution of receptor similarity (x-mean …
Figure 7
Transcriptional determinants of axon guidance molecules for individual receptor types.
(A) Correlation heatmap between receptor types calculated from co-expressed AG and TF genes. Receptor types are color-coded. (B) 3-D heatmap showing the Jaccard Indices between AG and TF genes for …
Tables
Key resources table
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Strain, strain background (Mus musculus; 2 females, 2 males) | C57BL/6 | In-house breeding | ||
| Strain, strain background (Mus musculus; 4 males, 4 females) | CD-1 | In-house breeding | ||
| Commercial assay or kit | Chromium Next GEM Single Cell 3’ GEM, Library and Gel Bead Kit v3.1 | 10 X Genomics | 1000120 | |
| Commercial assay or kit | ChromiumSingle Cell 3’ GEM, Library & Gel Bead Kit v3.0 | 10 X Genomics | 1000075 | |
| Commercial assay or kit | DNase I (RNase free) | NEB | M0303 | |
| Commercial assay or kit | Papain | Calbiochem | 5125 | |
| Commercial assay or kit | DAPI | Thermo Fisher Scientific | 62247 | |
| Commercial assay or kit | L-cysteine | Calbiochem | 243005 | |
| Commercial assay or kit | BSA | Sigma-Aldrich | A8806 | |
| Commercial assay or kit | Frozen section media | Leica | 3801481 | |
| Commercial assay or kit | DRAQ5 | Invitrogen | 65-0880-96 | |
| Commercial assay or kit | HBSS | VWR | VWRL0121-0500 | |
| Commercial assay or kit | PBS | Gibco | 10010023 | |
| Commercial assay or kit | Urethane | Sigma-Aldrich | U2500 | |
| Commercial assay or kit | NovaSeq S1 | Illumina | 20012865 | |
| software, algorithm | Fiji ImageJ | Goldstein et al., 2018 | https://imagej.net/software/fiji/ | |
| Software, algorithm | QuPath v0.4.3 | Bankhead et al., 2017 | https://qupath.github.io | |
| Software, algorithm | Seurat | Hao et al., 2021 | https://satijalab.org/seurat/ | |
| Software, algorithm | kallisto | bustools | Melsted et al., 2019 | https://www.kallistobus.tools | |
| Software, algorithm | DropletUtils | Lun et al., 2019 | https://bioconductor.org/packages/release/bioc/html/DropletUtils.html | |
| Software, algorithm | Illustrator | Adobe | https://www.adobe.com/illustrator | |
| Software, algorithm | SoupX | Young and Behjati, 2020 | https://cran.r-project.org/web/packages/SoupX/index.html | |
| Software, algorithm | clustree | Zappia and Oshlack, 2018 | https://cran.r-project.org/web/packages/clustree/index.html | |
| Software, algorithm | ggplot2 | Wickham et al., 2016 | https://cran.r-project.org/web/packages/ggplot2/index.html | |
| Software, algorithm | glmGamPoi | Ahlmann-Eltze and Huber, 2021 | https://bioconductor.org/packages/release/bioc/html/glmGamPoi.html | |
| Software, algorithm | vegan | Oksanen et al., 2019 | https://cran.r-project.org/web/packages/vegan/index.html | |
| Software, algorithm | Scrublet v0.2.3 | Wolock et al., 2019 | https://github.com/swolock/scrublet | |
| Software, algorithm | reticulate | Ushey et al., 2017 | https://cran.r-project.org/web/packages/reticulate/index.html | |
| Software, algorithm | GeneOverlap | Shen, 2019 | https://bioconductor.org/packages/release/bioc/html/GeneOverlap.html | |
| Software, algorithm | circlize | Gu et al., 2014 | https://cran.r-project.org/web/packages/circlize/index.html | |
| Software, algorithm | Slingshot | Street et al., 2018 | https://www.bioconductor.org/packages/release/bioc/html/slingshot.html | |
| Software, algorithm | tradeSeq | Van den Berge et al., 2020 | https://www.bioconductor.org/packages/release/bioc/html/tradeSeq.html | |
| Software, algorithm | msigdbr | Dolgalev, 2020 | https://cran.r-project.org/web/packages/msigdbr/vignettes/msigdbr-intro.html | |
| Software, algorithm | fgsea | Korotkevich et al., 2021 | https://bioconductor.org/packages/release/bioc/html/fgsea.html | |
| Software, algorithm | Molecular Cartography | Resolve Biosciences | https://resolvebiosciences.com/ |
