RT Journal Article
SR Electronic
T1 Gene-expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 207340
DO 10.1101/207340
A1 Joseph W. Foley
A1 Chunfang Zhu
A1 Philippe Jolivet
A1 Shirley X. Zhu
A1 Peipei Lu
A1 Michael J. Meaney
A1 Robert B. West
YR 2019
UL http://biorxiv.org/content/early/2019/05/24/207340.abstract
AB 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.