GSE106344
Lyophilized human cells stored at room temperature preserve multiple RNA species at excellent quality for RNA sequencing
Purpose: We aimed to examine whether eukaryotic cell lyophilization and long-term storage would be feasible as an environmentally friendly and cheap alternative to cryogenic storage or the use of FFPE samples for large-scale RNA profiling studies. Brief method: On three different days three million GM12873 cells were taken up in 0.1 M trehalose, subjected to lyophilization (freeze-drying) and then stored for two weeks at room temperature in the presence of CaCl2 in a dark, tightly sealed box. Fresh paired control cells were pelleted and taken up in trizol without lyophilization. Total RNA was isolated using a modified trizol method, quantified and subjected to mRNA-Seq library preparation. Samples were sequenced using a NextSeq 500 instrument to 75 bp (single-end). Raw reads were aligned to the hg19 genomic build with TopHat 2.0.7 and gene expression quantification was performed using Cufflinks. Results: We found that lyophilized cells are highly similar in all inferred RNA-Seq quality metrics compared to their non-lyophilized controls and are useful sources of high-quality RNA for both small and large-scale studies. Conslusion: Lyophilization might be the preservation technique of choice in the future for studies aiming to involve large sample sets, such as clinical studies. Overall design: mRNA profiles of three paired control and lyophilized cells stored at room temperature for two weeks.