title: Single-cell transcriptome conservation in cryopreserved cells and tissues.
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.
authors.affiliation: CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Barcelona, Spain.
authors.forename: Amy
authors.initials: A
authors.lastname: Guillaumet-Adkins
authors.affiliation: CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Barcelona, Spain.
authors.forename: Gustavo
authors.initials: G
authors.lastname: Rodríguez-Esteban
authors.affiliation: CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Barcelona, Spain.
authors.forename: Elisabetta
authors.initials: E
authors.lastname: Mereu
authors.affiliation: CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Barcelona, Spain.
authors.forename: Maria
authors.initials: M
authors.lastname: Mendez-Lago
authors.affiliation: Department of Immunology, Weizmann Institute, Rehovot, Israel.
authors.forename: Diego A
authors.initials: DA
authors.lastname: Jaitin
authors.affiliation: Chemoresistance and Predictive Factors Laboratory, Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), Barcelona, Spain.|Xenopat S.L., Business Bioincubator, Bellvitge Health Science Campus, Barcelona, Spain.
authors.forename: Alberto
authors.initials: A
authors.lastname: Villanueva
authors.affiliation: Department of Pathology, University Hospital of Bellvitge (IDIBELL), Barcelona, Spain.
authors.forename: August
authors.initials: A
authors.lastname: Vidal
authors.affiliation: Vall d'Hebron University Hospital, Barcelona, Spain.|Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.|Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain.
authors.forename: Alex
authors.initials: A
authors.lastname: Martinez-Marti
authors.affiliation: Vall d'Hebron University Hospital, Barcelona, Spain.|Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.|Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain.
authors.forename: Enriqueta
authors.initials: E
authors.lastname: Felip
authors.affiliation: Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain.
authors.forename: Ana
authors.initials: A
authors.lastname: Vivancos
authors.affiliation: Department of Immunology, Weizmann Institute, Rehovot, Israel.
authors.forename: Hadas
authors.initials: H
authors.lastname: Keren-Shaul
authors.affiliation: CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Barcelona, Spain.
authors.forename: Simon
authors.initials: S
authors.lastname: Heath
authors.affiliation: CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Barcelona, Spain.
authors.forename: Marta
authors.initials: M
authors.lastname: Gut
authors.affiliation: Department of Immunology, Weizmann Institute, Rehovot, Israel.
authors.forename: Ido
authors.initials: I
authors.lastname: Amit
authors.affiliation: CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Barcelona, Spain.
authors.forename: Ivo
authors.initials: I
authors.lastname: Gut
authors.affiliation: CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. holger.heyn@cnag.crg.eu.|Universitat Pompeu Fabra (UPF), Barcelona, Spain. holger.heyn@cnag.crg.eu.
authors.forename: Holger
authors.identifier: 0000-0002-3276-1889
authors.initials: H
authors.lastname: Heyn
mesh_terms: D000818:Animals; D002460:Cell Line; D016000:Cluster Analysis; D015925:Cryopreservation; D004195:Disease Models, Animal; D020869:Gene Expression Profiling / Q000379:methods; D064593:Heterografts; D006801:Humans; D051379:Mice; D009369:Neoplasms / Q000235:genetics / Q000473:pathology; D012313:RNA / Q000235:genetics; D020871:RNA Stability; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA; D059010:Single-Cell Analysis / Q000379:methods; D059467:Transcriptome
chemical_list: D012313:RNA
keywords: Conservation; Cryopreservation; MARS-Seq; PBMC; PDOX; Patient-derived orthotopic xenograft; Peripheral blood mononuclear cells; RNA sequencing; Single-cell genomics; Smart-seq2; Transcriptomics