Fig. 2

Correlating MARS-Seq-derived single-cell transcriptomes from fresh (red) and cryopreserved (blue) HEK293 cells identify subpopulations. a Pearson’s correlation analysis between 20 randomly selected fresh and cryopreserved cells displaying the correlation coefficient (r²). b Distribution of Pearson’s correlation coefficients (r²) within and between processing conditions. The median coefficients are indicated. c Pearson’s correlation analysis between 20 randomly selected fresh and cryopreserved HEK293 or K562 cells displaying the correlation coefficient (r²). d–f Linear regression model comparing average gene expression levels of (d) expressed, (e) cell cycle (G2/M checkpoint, and (f) apoptosis genes. The coefficient of determination (r²) is indicated. g Hierarchical clustering of single cells based on transcriptional programs (defined by Gene Ontology) and correlating gene sets [21]. Transcriptional programs and gene clusters are summarized in aspects. Displayed are the most variable aspects (rows) and their importance (row colors). Cells are assigned to condition (fresh: red; cryopreserved: blue) and clusters. h A t-SNE representation of similarities between cells using previous defined distances and cluster identity (as in g). Conditions are indicated (fresh: circle; cryopreserved: triangle). i Hierarchical cluster of single cells (as in g) displaying the 25 most variable cell cycle genes (G2/M checkpoint). Expression levels of the cell cycle signature are summarized (first panel; high: orange, low: green) and conditions (second panel; fresh: red; cryopreserved: blue) and clusters are indicated