Gene expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ
| Autor: | Shirley Zhu, Chunfang Zhu, Joseph W. Foley, Philippe Jolivet, Peipei Lu, Robert B. West, Michael J. Meaney |
|---|---|
| Rok vydání: | 2019 |
| Předmět: |
In situ
Sequence analysis Method Context (language use) Laser Capture Microdissection Computational biology Biology 03 medical and health sciences 0302 clinical medicine Gene expression Tumor Microenvironment Genetics Humans Genetics (clinical) Microdissection 030304 developmental biology Laser capture microdissection 0303 health sciences Sequence Analysis RNA Gene Expression Profiling Macrophages Reproducibility of Results RNA Gene expression profiling Single-Cell Analysis 030217 neurology & neurosurgery |
| Zdroj: | Genome Research. 29:1816-1825 |
| ISSN: | 1549-5469 1088-9051 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|