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Gene-expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ

View ORCID ProfileJoseph W Foley, Chunfang Zhu, Philippe Jolivet, Shirley X Zhu, Peipei Lu, Michael J Meaney, Robert B West
doi: https://doi.org/10.1101/207340
Joseph W Foley
Stanford University School of Medicine;
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  • For correspondence: jwfoley@stanford.edu
Chunfang Zhu
Stanford University School of Medicine;
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Philippe Jolivet
Université de Montréal;
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Shirley X Zhu
Stanford University School of Medicine;
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Peipei Lu
Stanford University School of Medicine;
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Michael J Meaney
McGill University
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Robert B West
Stanford University School of Medicine;
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Abstract

RNA sequencing (RNA-seq) is a sensitive and accurate method for quantifying gene expression. Small samples or those whose RNA is degraded, such as formalin-fixed, paraffin-embedded (FFPE) tissue, remain challenging to study with nonspecialized RNA-seq protocols. Here we present a new method, Smart-3SEQ, that accurately quantifies transcript abundance even with small amounts of total RNA and effectively characterizes small samples extracted by laser-capture microdissection (LCM) from FFPE tissue. We also obtain distinct biological profiles from FFPE single cells, which have been impossible to study with previous RNA-seq protocols, and we use these data to identify possible new macrophage phenotypes associated with the tumor microenvironment. We propose Smart-3SEQ as a highly cost-effective method to enable large gene-expression profiling experiments unconstrained by sample size and tissue availability. In particular, Smart-3SEQ's compatibility with FFPE tissue unlocks an enormous number of archived clinical samples, and combined with LCM it allows unprecedented studies of small cell populations and single cells isolated by their in situ context.

Footnotes

  • Figures S10, S12, S25 added. Panels added to Figures S26 and S28. Smart-seq 2014 published protocol added to Table S2 and Supplemental File 6. Figures 1 and S1 swapped. Various slight changes to text.

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Posted January 09, 2019.
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Gene-expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ
Joseph W Foley, Chunfang Zhu, Philippe Jolivet, Shirley X Zhu, Peipei Lu, Michael J Meaney, Robert B West
bioRxiv 207340; doi: https://doi.org/10.1101/207340
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Gene-expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ
Joseph W Foley, Chunfang Zhu, Philippe Jolivet, Shirley X Zhu, Peipei Lu, Michael J Meaney, Robert B West
bioRxiv 207340; doi: https://doi.org/10.1101/207340

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