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

Single-cell transcriptome conservation in cryopreserved cells and tissues.

Author information

1
CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
2
Universitat Pompeu Fabra (UPF), Barcelona, Spain.
3
Department of Immunology, Weizmann Institute, Rehovot, Israel.
4
Chemoresistance and Predictive Factors Laboratory, Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), Barcelona, Spain.
5
Xenopat S.L., Business Bioincubator, Bellvitge Health Science Campus, Barcelona, Spain.
6
Department of Pathology, University Hospital of Bellvitge (IDIBELL), Barcelona, Spain.
7
Vall d'Hebron University Hospital, Barcelona, Spain.
8
Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.
9
Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain.
10
CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. holger.heyn@cnag.crg.eu.
11
Universitat Pompeu Fabra (UPF), Barcelona, Spain. holger.heyn@cnag.crg.eu.

Abstract

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

PMID:
28249587
PMCID:
PMC5333448
DOI:
10.1186/s13059-017-1171-9
[Indexed for MEDLINE]
Free PMC Article

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