PT  - JOURNAL ARTICLE
AU  - Joseph W. Foley
AU  - Chunfang Zhu
AU  - Philippe Jolivet
AU  - Shirley X. Zhu
AU  - Peipei Lu
AU  - Michael J. Meaney
AU  - Robert B. West
TI  - Gene-expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ
AID  - 10.1101/207340
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 207340
4099  - http://biorxiv.org/content/early/2018/01/11/207340.short
4100  - http://biorxiv.org/content/early/2018/01/11/207340.full
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 scalable 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.