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High fidelity hypothermic preservation of primary tissues in organ transplant preservative for single cell transcriptome analysis

By Wanxin Wang, Lolita Penland, Ozgun Gokce, Derek Croote, Stephen Quake

Posted 10 Mar 2017
bioRxiv DOI: 10.1101/115733 (published DOI: 10.1186/s12864-018-4512-5)

Background High-fidelity preservation strategies for primary tissues are in great demand in the single cell RNAseq community. A reliable method will greatly expand the scope of feasible collaborations and maximize the utilization of technical expertise. When choosing a method, standardizability is as important a factor to consider as fidelity due to the susceptibility of single-cell RNAseq analysis to technical noises. Existing approaches such as cryopreservation and chemical fixation are less than ideal for failing to satisfy either or both of these standards. Results Here we propose a new strategy that leverages preservation schemes developed for organ transplantation. We evaluated the strategy by storing intact mouse kidneys in organ transplant preservative solution at hypothermic temperature for up to 4 days (6 hrs, 1, 2, 3, or 4 days), and comparing the quality of preserved and fresh samples using FACS and single-cell RNAseq. We demonstrate that the strategy effectively maintained cell viability, transcriptome integrity, cell population heterogeneity, and transcriptome landscape stability for samples after up to 3 days of preservation. The strategy also facilitated the definition of the diverse spectrum of kidney resident immune cells, to our knowledge the first time at single cell resolution. Conclusions Hypothermic storage of intact primary tissues in organ transplant preservative maintains the quality and stability of the transcriptome of cells for single cell RNAseq analysis. The strategy is readily generalizable to primary specimens from other tissue types for single cell RNAseq analysis.

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