Additional file 4 of Cryopreservation of human cancers conserves tumour heterogeneity for single-cell multi-omics analysis

Additional file 4. Cluster metrics and annotations. Cluster metric standard deviations, cluster annotations, cluster gene correlations and gene pathways conserved across cryopreserved conditions. a, Standard deviations for silhouette scores, mixing metrics and local structure metrics, computed for the comparisons between the down sampled cells from Fresh Tissue (FT) with cells from FT (positive control), Cryopreserved Cell Suspensions (CCS), Cryopreserved Tissue (CT) and Cryopreserved Overnight (CO). b, Integrated cluster annotations. c, Cluster level correlation values. Adjusted-R2 values computed using linear regression in R to model log-normalised gene expression values between integrated clustered cells from different cryopreserved replicates. d, Conservation of cluster Gene Ontology (GO) pathways following cryopreservation. Functional enrichment was first performed for all differentially expressed genes in each integrated cluster in FT samples. Enrichment scores for these pathways were then compared to the respective integrated cluster in each cryopreserved replicate (CCS, CT, CO). All DEGs from each cluster were passed on to the ClusterProfiler package for functional enrichment with the CC sub-ontology under the human org.Hs.eg.db database. Specific GO pathways that were unique to FT clusters, CCS vs CT clusters or CT vs CCS clusters are listed with the cluster and number of tumours that they were identified in.