Table 1.

Summary of the Main Similarities and Differences in Study Design, Sample Preparation, Single-Cell RNA Sequencing Strategies, and Bioinformatic Analysis Pipelines between the 3 Studies.

Study	Sharir et al. (2019)	Krivanek et al. (2020)	Chiba et al. (2020)
Species	Mouse	Mouse a	Mouse
Strain	C57BL/6N	C57BL/6N; Sox2-RFP	Krt14-RFP
Age	8 wk	2–4 mo	7 d
Sex	Males	Males and females	Not stated
Number of individuals	5	39	7
Tooth	Incisor	Incisor a	Incisor
Region	Proximal region	Entire tooth	Entire tooth
Dissociation enzyme	Collagenase P	Collagenase P	Dispase II
Strategy to reduce the impact of cellular stress	FACS with live/dead stain + mitochondrial gene expression regression	Rapid FACS sorting of cells onto plates	No FACS sorting + mitochondrial gene expression regression
Number of analyzed cells	3,173	2,889	6,260 b
scRNA-seq strategy	10× Chromium	Smart-seq2	10× Chromium
Clustering method	Spectral clustering of a K-nearest neighbor graph	Hierarchical clustering using Ward method and Pearson correlation distance (PAGODA)	Hierarchical clustering based on Euclidean distance and complete linkage (Seurat)
Visualization	SPRING (Weinreb et al. 2018)	t-SNE	t-SNE

FACS, Fluorescence Activated Cell Sorter; scRNA-seq, single-cell RNA sequencing; t-SNE, t-distributed stochastic neighbor embedding.

^aKrivanek et al. (2020) also sequenced the incisor mesenchyme, the mouse first molar, and human wisdom tooth.

^bIncluding the mesenchyme and immune cells.