Fig. 2

Comparison of global gene expression in scRNAseq and snRNAseq data. A Number of reads found in nuclei (Y-axis) over the number of reads of those same genes found in cells (Y-axis) based on normalized datasets. Ribosomal genes are highlighted in blue, mitochondrial genes are shown in yellow and heat shock genes are shown in red. Ribosomal genes are defined as genes starting RpS- or RpL- and heat shock genes are defined as genes encoding heat shock proteins, starting with Hsp-. B, C Variable feature plot of scRNAseq B and snRNAseq data C of dissociated cells and nuclei, respectively. The top 10 variable genes of the scRNAseq dataset are labeled in red and the top 10 variable genes of the snRNAseq dataset are labeled in blue. These genes are the ones having the strongest influence on clustering and cell type identification for the respective dataset (see also Fig. 3). The top 3000 genes (yellow dots) are used for subsequent cluster analyses. D Venn-diagram of the top 3000 variable genes in scRNAseq, snRNAseq and the overlap of both datasets. See also Additional file 9: Table S9 for a full list of genes in each category