Molecular and spatial profiling of the paraventricular nucleus of the thalamus
- National Institute of Mental Health, United States
- Department of Neuroscience, Brown University, United States
- National Institute on Alcohol Abuse and Alcoholism, United States
- National Institute of Child Health and Human Development, United States
Figures
Figure 1 with 2 supplements
Single-nucleus RNA-sequencing in and around the mouse paraventricular nucleus of the thalamus (PVT).
(a) Sagittal view of the PVT (red) illustrating the dissection target location. (b) Distribution of nuclei from four samples across all cell types. (c) The uniform manifold approximation and …
Figure 1—figure supplement 1
Quality control statistics and uniform manifold approximation and projection (UMAP) by sample.
(a–c) Violin plots depicting the percent mitochondrial RNA (a), number of UMIs (b), and the number of genes (c) detected by sample. (d) The UMAP plot of the same nuclei from Figure 1c is labeled by …
Figure 1—figure supplement 2
Clustering analysis and classification of all neurons.
(a) The uniform manifold approximation and projection (UMAP) plot of 9845 neuronal nuclei shows nine clusters. (b) Feature plots of representative gene expression of markers from different clusters. …
Figure 2 with 1 supplement
Five transcriptionally distinct neuronal subtypes are found in the paraventricular nucleus of the thalamus (PVT).
(a) The uniform manifold approximation and projection (UMAP) plot of 5737 PVT neuronal nuclei shows five clusters. (b) Phylogenetic tree depicting cluster relationships based on the distance between …
Figure 2—figure supplement 1
Drd2 expression is found in PVT1 and PVT2.
(a) The uniform manifold approximation and projection (UMAP) plot of 4067 paraventricular nucleus of the thalamus (PVT) neuronal nuclei shows five clusters. (b) Feature plot of Drd2 expression …
Figure 3 with 3 supplements
Mapping of five paraventricular nucleus of the thalamus (PVT) subtypes reveals a gradient-like segregated distribution.
(a) RNA in situ hybridization in anterior PVT (white dotted outline) with closeup insert (right, yellow square) labeling one gene marker from each subtype: Esr1 (light blue), Col12a1 (red), Npffr1 …
Figure 3—figure supplement 1
Spatial distribution and overlap across anterior- or posterior- and pan-PVT subtypes.
(a) Dendrogram depicting Euclidian distance between cluster types based on gene transcript expression. (b–c) Location of positive cells expressing Esr1 (blue square), Col12a1 (black circle), and Drd3…
Figure 3—figure supplement 2
Overlap in gene expression among top markers from the same cluster.
(a–b) Location of Esr1 (black) or Drd2 (red) positive cells in aPVT (a) or pPVT (b) from PVT1 subtype. (c) Venn diagram of cell count and percent overlap between Esr1- and Drd2-positive cells. (d-e) …
Figure 3—figure supplement 3
In situ hybridization of top markers from the same cluster.
(a) In situ hybridization of Esr1 (green), Drd2 (magenta), and DAPI (blue) in pPVT (white outline). (b–d) Yellow square insert from (a). (e) In situ hybridization of Col12a1 (green), Pde3a …
Figure 4
Five paraventricular nucleus of the thalamus (PVT) subtypes have diverse neuromodulator receptor, neuromodulator, and ion channel expression.
(a) Dot plot depicting neuromodulator receptor gene expression across five PVT subtypes. (b) Dot plot depicting ion channel gene expression across five PVT subtypes. (c) Dot plot depicting …
Figure 5 with 4 supplements
Cross-validation with ThalamoSeq dataset reveals overlap between paraventricular nucleus of the thalamus (PVT) subtypes and thalamic cortical projectors.
(a) The uniform manifold approximation and projection (UMAP) plot of 7709 cells or nuclei from combined datasets annotated by cluster identity. (b) The same cells/nuclei are separated by the study …
Figure 5—figure supplement 1
RPCA-based integration with ThalamoSeq dataset and all neurons from the present study reveals mostly non-overlapping transcriptomes.
(a) The uniform manifold approximation and projection (UMAP) plot of 11,817 cells or nuclei from combined datasets annotated by cluster identity. (b) The same cells/nuclei are separated by the study …
Figure 5—figure supplement 2
PL-projecting pPVT neurons are localized to the ventroposterior edge of the paraventricular nucleus of the thalamus (PVT) and partially overlap with Col12a1.
(a) Representative image of the injection site of green fluorescent retrobeads in the prelimbic cortex (PL). (b–e) Representative image of the localization of retrobeads (green) and Col12a1 mRNA …
Figure 5—figure supplement 3
Dual anterograde and retrograde tracing from the prelimbic cortex (Mouse Connectome Project Experiment SW120125-02A).
(a–c) Representative image of the injection site in the prelimbic cortex (PL) of retrograde tracer CTB647 (magenta) and anterograde tracer PHAL (green); Scale bar 1 mm. (d-f) Representative image of …
Figure 5—figure supplement 4
Projections from aPVT to Auditory and Visual cortical areas.
(a) Schematic of Target Search tool used to identify experiments where projections from the PVT to Auditory (AUD) and Visual (VIS) areas were detected (Mouse Brain Connectivity Atlas of the Allen …
Author response image 1
Author response image 2
Author response image 3
Additional files
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MDAR checklist
- https://cdn.elifesciences.org/articles/81818/elife-81818-mdarchecklist1-v2.pdf
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Supplementary file 1
Lists of differential gene expression for snRNA-seq data and conserved marker analysis from the integrated dataset.
- https://cdn.elifesciences.org/articles/81818/elife-81818-supp1-v2.xlsx
