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

Ditte Lovatt, Brittani K. Ruble, Jaehee Lee, Hannah Dueck, Tae Kyung Kim, Stephen Fisher, Chantal Francis, Jennifer M. Spaethling, John A. Wolf, M. Sean Grady, Alexandra V. Ulyanova, Sean B. Yeldell, Julianne C. Griepenburg, Peter T. Buckley, Junhyong Kim, Jai Yoon Sul, Ivan J. Dmochowski, James Eberwine

Research output: Contribution to journalArticlepeer-review

152 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)190-196
Number of pages7
JournalNature Methods
Volume11
Issue number2
DOIs
StatePublished - Feb 2014
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Biochemistry
  • Molecular Biology
  • Cell Biology

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