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

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; combined with LCM it allows unprecedented studies of small cell populations and single cells isolated by their in situ context.

journal_name

Genome Res

journal_title

Genome research

authors

Foley JW,Zhu C,Jolivet P,Zhu SX,Lu P,Meaney MJ,West RB

doi

10.1101/gr.234807.118

subject

Has Abstract

pub_date

2019-11-01 00:00:00

pages

1816-1825

issue

11

eissn

1088-9051

issn

1549-5469

pii

gr.234807.118

journal_volume

29

pub_type

杂志文章

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