Single-cell transcriptome conservation in cryopreserved cells and tissues

Genome Biol. 2017 Mar 1;18(1):45. doi: 10.1186/s13059-017-1171-9.


A variety of single-cell RNA preparation procedures have been described. So far, protocols require fresh material, which hinders complex study designs. We describe a sample preservation method that maintains transcripts in viable single cells, allowing one to disconnect time and place of sampling from subsequent processing steps. We sequence single-cell transcriptomes from >1000 fresh and cryopreserved cells using 3'-end and full-length RNA preparation methods. Our results confirm that the conservation process did not alter transcriptional profiles. This substantially broadens the scope of applications in single-cell transcriptomics and could lead to a paradigm shift in future study designs.

Keywords: Conservation; Cryopreservation; MARS-Seq; PBMC; PDOX; Patient-derived orthotopic xenograft; Peripheral blood mononuclear cells; RNA sequencing; Single-cell genomics; Smart-seq2; Transcriptomics.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cell Line
  • Cluster Analysis
  • Cryopreservation*
  • Disease Models, Animal
  • Gene Expression Profiling* / methods
  • Heterografts
  • Humans
  • Mice
  • Neoplasms / genetics
  • Neoplasms / pathology
  • RNA / genetics
  • RNA Stability
  • Reproducibility of Results
  • Sequence Analysis, DNA
  • Single-Cell Analysis* / methods
  • Transcriptome*


  • RNA