@article{Foley01112019,
author = {Foley, Joseph W. and Zhu, Chunfang and Jolivet, Philippe and Zhu, Shirley X. and Lu, Peipei and Meaney, Michael J. and West, Robert B.}, 
title = {Gene expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ},
volume = {29}, 
number = {11}, 
pages = {1816-1825}, 
year = {2019}, 
doi = {10.1101/gr.234807.118}, 
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.}, 
URL = {http://genome.cshlp.org/content/29/11/1816.abstract}, 
eprint = {http://genome.cshlp.org/content/29/11/1816.full.pdf+html}, 
journal = {Genome Research} 
}