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Fig. 5 | Genome Biology

Fig. 5

From: Single-cell transcriptome conservation in cryopreserved cells and tissues

Fig. 5

Correlating single-cell transcriptome data from fresh (red) and cryopreserved (blue) samples determines cell subtypes in PBMC. a, b Comparative analysis of the number of sequencing reads and detected transcripts (a) or genes (b) per cell 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 (see “Material and methods”) 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 (BC B-cells, CytoTC cytotoxic T-cells, MemTC memory T-cells, Myd myeloid 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 conditions (first panel: fresh: red; cryopreserved: blue) and clusters

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