TY  - JOUR
A1  - Foley, Joseph W.
A1  - Zhu, Chunfang
A1  - Jolivet, Philippe
A1  - Zhu, Shirley X.
A1  - Lu, Peipei
A1  - Meaney, Michael J.
A1  - West, Robert B.
T1  - Gene expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ
Y1  - 2019/11/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 1816 
EP  - 1825 
DO  - 10.1101/gr.234807.118 
VL  - 29 
IS  - 11 
UR  - http://genome.cshlp.org/content/29/11/1816.abstract 
N2  - 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. 
ER  -