Multi-omic measurements of heterogeneity in HeLa cells across laboratories

We collected 14 stock Hela aliquots from 13 different laboratories across the globe and cultured them in the same conditions. We extensively profiled the genome-wide copy numbers, mRNAs, proteins, protein turnover rates by genomics techniques and the highly reproducible and accurate proteomic method, SWATH mass spectrometry. The cell lines were also phenotyped with respect to the ability of transfected Let7 mimics to modulate Salmonella infection. We discovered significant heterogeneity between Hela variants especially differences between the CCL2 and Kyoto lines collected from different sites. In addition, we observed progressive divergence within a specific cell line over 50 successive passages. By associating proteotype and phenotype we identified molecular patterns that varied between cell lines and explained varying responses to Salmonella infection across the cells. The results furthermore quantify how the cells respond to genomic variability across the transcriptome and proteome.