Access to raw single-cell RNA-seq datasets and count matrices:

All single-cell RNA-seq datasets have been deposited in the GEO under accession code GSE146123

General mouse incisor atlas

• Interactive PAGODA visualization view
• RDS file with the analysis information download
• Data resource:
• count matrix download
• tSNE embedding download
• cluster annotation download
• Average gene expression levels per cluster can be downloaded as xls file or visualized as heatmap
• Folder with all resource data can be explored here

Compartments of mouse incisor

Epithelial compartment

• Interactive PAGODA visualization view
• RDS file with the analysis information download
• Data resource:
• count matrix download
• tSNE embedding download
• cluster annotation download
• Average gene expression levels per cluster can be downloaded as xls file or visualized as heatmap
• Folder with all resource data can be explored here

Mesenchymal compartment

• Interactive PAGODA visualization view
• RDS file with the analysis information download
• Data resource:
• count matrix download
• tSNE embedding download
• cluster annotation download
• Average gene expression levels per cluster can be downloaded as xls file or visualized as heatmap
• Gene patterns along distal pulp trajectory are visualized as heatmap
and summary statistics on individual genes can be downloaded here
• Gene patterns along peri-odontoblastic pulp trajectory are visualized as heatmap
and summary statistics on individual genes can be downloaded here
• Gene patterns along odontoblastic trajectory are visualized as heatmap
• Folder with all resource data can be explored here

Immune compartment

• Interactive PAGODA visualization view
• RDS file with the analysis information download
• Data resource:
• count matrix download
• tSNE embedding download
• cluster annotation download
• Average gene expression levels per cluster can be downloaded as xls file or visualized as heatmap
• Folder with all resource data can be explored here

Other compartments

• Endothelium: Average gene expression levels per cluster can be downloaded as xls file or visualized as heatmap
• Glia: Average gene expression levels per cluster can be downloaded as xls file or visualized as heatmap
• Pericytes: Average gene expression levels per cluster can be downloaded as xls file or visualized as heatmap
• Extra-pulp: Average gene expression levels per cluster can be downloaded as xls file or visualized as heatmap

Comparative map of mouse incisor and molar teeth

• Interactive PAGODA2 visualization view
• RDS file with the analysis information download
• Data resource:
• count matrix download
• tSNE embedding download
• cluster annotation download
• Consensus list of differentially expressed genes between distal incisor pulp and molar pulp (mean log2 fold change of gene expression) can be downloaded here (here can be found summary statistics on differential expression for all genes separately for 10x Chromium data and Smart-seq2 data)
• Folder with all resource data can be explored here

Human adult and growing molar teeth

• Interactive PAGODA2 visualization view
• RDS file with the analysis information download
• Data resource:
• count matrix download
• tSNE embedding download
• cluster annotation download
• Average gene expression levels across pulp clusters can be downloaded here
• Folder with all resource data can be explored here

Code availability:

Analysis scripts are used for the preparation of the manuscript can be found here

All other code is available upon request.