Analysis of public RNA-sequencing data reveals biological consequences of genetic heterogeneity in cell line populations.

ABSTRACT: Meta-analysis of datasets available in public repositories are used to gather and summarise experiments performed across laboratories, as well as to explore consistency of scientific findings. As data quality and biological equivalency across samples may obscure such analyses and consequently their conclusions, we investigated the comparability of 85 public RNA-seq cell line datasets. Thousands of pairwise comparisons of single nucleotide variants in 139 samples revealed variable genetic heterogeneity of the eight cell line populations analysed as well as variable data quality. The H9 and HCT116 cell lines were found to be remarkably stable across laboratories (with median concordances of 99.2% and 98.5%, respectively), in contrast to the highly variable HeLa cells (89.3%). We show that th

SUBMITTER: Fasterius E 

PROVIDER: S-EPMC6060100 | biostudies-literature | 2018 Jul

REPOSITORIES: biostudies-literature