Gene expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ
| العنوان: | Gene expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ |
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| المؤلفون: | Shirley Zhu, Chunfang Zhu, Joseph W. Foley, Philippe Jolivet, Peipei Lu, Robert B. West, Michael J. Meaney |
| المصدر: | Genome Research. 29:1816-1825 |
| بيانات النشر: | Cold Spring Harbor Laboratory, 2019. |
| سنة النشر: | 2019 |
| مصطلحات موضوعية: | 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 |
| الوصف: | 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. |
| تدمد: | 1549-5469 1088-9051 |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a9c058204cf5ebd3f737a6c3e3290baa https://doi.org/10.1101/gr.234807.118 |
| حقوق: | OPEN |
| رقم الأكسشن: | edsair.doi.dedup.....a9c058204cf5ebd3f737a6c3e3290baa |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 15495469 10889051 |
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