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Nat Methods. 2014 Feb;11(2):190-6. doi: 10.1038/nmeth.2804. Epub 2014 Jan 12.

Transcriptome in vivo analysis (TIVA) of spatially defined single cells in live tissue.

Author information

1
1] Department of Pharmacology, University of Pennsylvania, Philadelphia, Pennsylvania, USA. [2].
2
1] Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA. [2].
3
Department of Pharmacology, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
4
Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
5
Department of Neurosurgery, University of Pennsylvania Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
6
Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
7
1] Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA. [2] PENN Genome Frontiers Institute, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
8
1] Department of Pharmacology, University of Pennsylvania, Philadelphia, Pennsylvania, USA. [2] PENN Genome Frontiers Institute, University of Pennsylvania, Philadelphia, Pennsylvania, USA. [3].

Abstract

Transcriptome profiling of single cells resident in their natural microenvironment depends upon RNA capture methods that are both noninvasive and spatially precise. We engineered a transcriptome in vivo analysis (TIVA) tag, which upon photoactivation enables mRNA capture from single cells in live tissue. Using the TIVA tag in combination with RNA sequencing (RNA-seq), we analyzed transcriptome variance among single neurons in culture and in mouse and human tissue in vivo. Our data showed that the tissue microenvironment shapes the transcriptomic landscape of individual cells. The TIVA methodology is, to our knowledge, the first noninvasive approach for capturing mRNA from live single cells in their natural microenvironment.

PMID:
24412976
PMCID:
PMC3964595
DOI:
10.1038/nmeth.2804
[Indexed for MEDLINE]
Free PMC Article

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