Fig. 2

Transcriptome integrities and gene expression levels are preserved in fixed cells. a Drop-seq of mixed human and mouse cells (50 cells/μl). Plots show the number of human and mouse transcripts (UMIs) associated with a cell (dot) identified as human- or mouse-specific (blue or red, respectively). Cells expressing fewer than 3500 UMIs are grey; doublets are violet. b Distribution and the median of the number of genes and transcripts (UMIs) detected per cell (>3500 UMIs). Libraries were sequenced to a median depth of ~20,500 (Live) and ~15,500 (Fixed) aligned reads per cell. c Gene expression levels from live and fixed cells correlate well. Pairwise correlations between bulk mRNA-seq libraries and Drop-seq single-cell experiments. Non-single cell bulk mRNA-seq data were expressed as reads per kilobase per million (RPKM). Drop-seq expression counts were converted to average transcripts per million (ATPM) and plotted as log2 (ATPM + 1). Upper right panels show Pearson correlation. The overlap (common set) between all five samples is high (17,326 genes). Experiments with live and fixed cells were independently repeated with similar results (unpublished)