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Fig. 3 | Genome Biology

Fig. 3

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

Fig. 3

Comparative analyses of Smart-seq2-derived single-cell transcriptomes from fresh (red) and cryopreserved (blue) HEK293 cells. a Sequencing read distribution following RNA library preparation of full-length transcripts. Each line represents a single cell and transcript sizes are scaled from 0 to 100. b Cumulative gene counts split by fresh and cryopreserved cells and analyzed using randomly sampled cells (average of 100 permutations). c, d Gene expression variances of single cells displayed as PCA (c) or t-SNE representation (d) using the 100 most variable genes. e Pearson’s correlation analysis between 20 randomly selected fresh and cryopreserved cells displaying the correlation coefficient (r2). f Distribution of Pearson’s correlation coefficients (r2) within and between processing conditions. The median coefficients are 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 conditions (fresh: red; cryopreserved: blue) and clusters. h A t-SNE representation of similarities between cells using previous defined distances and cluster identities (as in g). Conditions are indicated (fresh: circle; cryopreserved: triangle). i Hierarchical clustering (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

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