Fig. 6

Single-cell transcriptome data from fresh (red) and cryopreserved (blue) mouse colon cells. a, b Comparative analysis of the number of sequencing reads and detected transcripts (a) or genes (b) using a linear model. The slope of the regression line was calculated separately for fresh and cryopreserved cells. c Cumulative gene counts split by fresh and cryopreserved cells and analyzed using randomly sampled cells (average of 100 permutations). d Linear regression model comparing average gene expression levels of expressed genes. The coefficient of determination (r²) is indicated. e Gene expression variances displayed as t-SNE representation using the 100 most variable genes. f 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. g A t-SNE representation of similarities between cells using distances and cluster identities (as in f). Conditions are indicated (fresh: circle; cryopreserved: triangle). Cell types were annotated based on marker gene expression [9] (TA transit amplifying, ECpr enterocytes precursors, EC enterocytes, SC secretory cells). h Hierarchical clustering of single cells (as in f). Displayed are the expression levels of the 25 most variable genes implicated in cluster formation. Cells are assigned to condition (first panel: fresh: red; cryopreserved: blue) and clusters