Extended Data Fig. 3: Annotation of cell types by Paired-Tag transcriptomic profiles.
From: Joint profiling of histone modifications and transcriptome in single cells from mouse brain
a, UMAP embedding of Paired-Tag transcriptomic profiles and stacked bar plots showing the fraction of cells from different regions or replicates (dissections from different mice) in each cell type. b, UMAP embedding of transcriptomic profiles from individual Paired-Tag and Paired-seq datasets. The color of cell types was the same as in Fig.1d. c, Dot plots showing the expression of marker genes for each mouse brain cell type measured from Paired-Tag RNA profiles. The size of the dots represents the fraction of cells positively detect the transcripts and the color of the dots represents the average. d, UMAPs showing the co-embedding of single-nucleus gene expression from Paired-Tag RNA profiles and the previously published scRNA-seq datasets of the same tissues. e, Heatmaps showing the confusion matrices of the overlap between cell type annotations based on Paired-Tag RNA profiles and from the previously published scRNA-seq datasets. The circles left side indicating RNA clusters and were colored according to Fig.1d. f, Boxplots showing the Pearson’s correlation coefficients for all genes, variable genes and invariable genes for matched and non-matched cell types between Paired-Tag RNA profiles and the previously published scRNA-seq. The boxes were drawn from lower quartile (Q1) to upper quartile (Q3) with the middle line denote the median, whiskers with maximum 1.5 IQR, outliers were indicated with dots. n = 22 cell types. g, Scatter plot showing the expression levels of variable genes in Astrocytes measured by Paired-Tag RNA profiles and the published scRNA-seq datasets.
