Sep 6, 2014

The effect of freeze-thaw cycles on gene expression levels in lymphoblastoid cell lines

PloS One
Minal ÇalışkanYoav Gilad

Abstract

Epstein-Barr virus (EBV) transformed lymphoblastoid cell lines (LCLs) are a widely used renewable resource for functional genomic studies in humans. The ability to accumulate multidimensional data pertaining to the same individual cell lines, from complete genomic sequences to detailed gene regulatory profiles, further enhances the utility of LCLs as a model system. However, the extent to which LCLs are a faithful model system is relatively unknown. We have previously shown that gene expression profiles of newly established LCLs maintain a strong individual component. Here, we extend our study to investigate the effect of freeze-thaw cycles on gene expression patterns in mature LCLs, especially in the context of inter-individual variation in gene expression. We report a profound difference in the gene expression profiles of newly established and mature LCLs. Once newly established LCLs undergo a freeze-thaw cycle, the individual specific gene expression signatures become much less pronounced as the gene expression levels in LCLs from different individuals converge to a more uniform profile, which reflects a mature transformed B cell phenotype. We found that previously identified eQTLs are enriched among the relatively few genes...Continue Reading

Mentioned in this Paper

Thaw
Real-Time Polymerase Chain Reaction
Biochemical Pathway
Microarray Analysis
T-Lymphocyte
Cortex Bone Disorders
Adrenal Cortex Diseases
Specimen Type - Fibroblasts
Genome
DNA, Mitochondrial

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