Single-cell transcriptome conservation in cryopreserved cells and tissues

Amy Guillaumet-Adkins; Gustavo Rodríguez-Esteban; Elisabetta Mereu; Maria Mendez-Lago; Diego A. Jaitin; Alberto Villanueva; August Vidal; Alex Martinez-Marti; Enriqueta Felip; Ana Vivancos; Hadas Keren-Shaul; Simon Heath; Marta Gut; Ido Amit; Ivo Gut; Holger Heyn

doi:10.1186/s13059-017-1171-9

Single-cell transcriptome conservation in cryopreserved cells and tissues

Amy Guillaumet-Adkins, Gustavo Rodríguez-Esteban, Elisabetta Mereu, Maria Mendez-Lago, Diego A. Jaitin, Alberto Villanueva, August Vidal, Alex Martinez-Marti, Enriqueta Felip, Ana Vivancos, Hadas Keren-Shaul, Simon Heath, Marta Gut, Ido Amit, Ivo Gut, Holger Heyn

Department of Medicine

Research output: Contribution to journal › Article › Research › peer-review

60 Citations (Scopus)

Abstract

© 2017 The Author(s). 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.

Original language	English
Article number	45
Journal	Genome Biology
Volume	18
Issue number	1
DOIs	https://doi.org/10.1186/s13059-017-1171-9
Publication status	Published - 1 Mar 2017

Keywords

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

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Guillaumet-Adkins, A., Rodríguez-Esteban, G., Mereu, E., Mendez-Lago, M., Jaitin, D. A., Villanueva, A., Vidal, A., Martinez-Marti, A., Felip, E., Vivancos, A., Keren-Shaul, H., Heath, S., Gut, M., Amit, I., Gut, I., & Heyn, H. (2017). Single-cell transcriptome conservation in cryopreserved cells and tissues. Genome Biology, 18(1), [45]. https://doi.org/10.1186/s13059-017-1171-9

Guillaumet-Adkins, Amy ; Rodríguez-Esteban, Gustavo ; Mereu, Elisabetta ; Mendez-Lago, Maria ; Jaitin, Diego A. ; Villanueva, Alberto ; Vidal, August ; Martinez-Marti, Alex ; Felip, Enriqueta ; Vivancos, Ana ; Keren-Shaul, Hadas ; Heath, Simon ; Gut, Marta ; Amit, Ido ; Gut, Ivo ; Heyn, Holger. / Single-cell transcriptome conservation in cryopreserved cells and tissues. In: Genome Biology. 2017 ; Vol. 18, No. 1.

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abstract = "{\textcopyright} 2017 The Author(s). 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, Patient-derived orthotopic xenograft, PBMC, PDOX, Peripheral blood mononuclear cells, RNA sequencing, Single-cell genomics, Smart-seq2, Transcriptomics",

author = "Amy Guillaumet-Adkins and Gustavo Rodr{\'i}guez-Esteban and Elisabetta Mereu and Maria Mendez-Lago and Jaitin, {Diego A.} and Alberto Villanueva and August Vidal and Alex Martinez-Marti and Enriqueta Felip and Ana Vivancos and Hadas Keren-Shaul and Simon Heath and Marta Gut and Ido Amit and Ivo Gut and Holger Heyn",

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Guillaumet-Adkins, A, Rodríguez-Esteban, G, Mereu, E, Mendez-Lago, M, Jaitin, DA, Villanueva, A, Vidal, A, Martinez-Marti, A, Felip, E, Vivancos, A, Keren-Shaul, H, Heath, S, Gut, M, Amit, I, Gut, I & Heyn, H 2017, 'Single-cell transcriptome conservation in cryopreserved cells and tissues', Genome Biology, vol. 18, no. 1, 45. https://doi.org/10.1186/s13059-017-1171-9

Single-cell transcriptome conservation in cryopreserved cells and tissues. / Guillaumet-Adkins, Amy; Rodríguez-Esteban, Gustavo; Mereu, Elisabetta; Mendez-Lago, Maria; Jaitin, Diego A.; Villanueva, Alberto; Vidal, August; Martinez-Marti, Alex; Felip, Enriqueta; Vivancos, Ana; Keren-Shaul, Hadas; Heath, Simon; Gut, Marta; Amit, Ido; Gut, Ivo; Heyn, Holger.

In: Genome Biology, Vol. 18, No. 1, 45, 01.03.2017.

Research output: Contribution to journal › Article › Research › peer-review

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AU - Guillaumet-Adkins, Amy

AU - Rodríguez-Esteban, Gustavo

AU - Mereu, Elisabetta

AU - Mendez-Lago, Maria

AU - Jaitin, Diego A.

AU - Villanueva, Alberto

AU - Vidal, August

AU - Martinez-Marti, Alex

AU - Felip, Enriqueta

AU - Vivancos, Ana

AU - Keren-Shaul, Hadas

AU - Heath, Simon

AU - Gut, Marta

AU - Amit, Ido

AU - Gut, Ivo

AU - Heyn, Holger

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N2 - © 2017 The Author(s). 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.

AB - © 2017 The Author(s). 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.

KW - Conservation

KW - Cryopreservation

KW - MARS-Seq

KW - Patient-derived orthotopic xenograft

KW - PBMC

KW - PDOX

KW - Peripheral blood mononuclear cells

KW - RNA sequencing

KW - Single-cell genomics

KW - Smart-seq2

KW - Transcriptomics

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DO - 10.1186/s13059-017-1171-9

M3 - Article

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