title: Transcriptome in vivo analysis (TIVA) of spatially defined single cells in live tissue.
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.
authors.affiliation: 1] Department of Pharmacology, University of Pennsylvania, Philadelphia, Pennsylvania, USA. [2].
authors.forename: Ditte
authors.initials: D
authors.lastname: Lovatt
authors.affiliation: 1] Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA. [2].
authors.forename: Brittani K
authors.initials: BK
authors.lastname: Ruble
authors.affiliation: Department of Pharmacology, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
authors.forename: Jaehee
authors.initials: J
authors.lastname: Lee
authors.affiliation: Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
authors.forename: Hannah
authors.initials: H
authors.lastname: Dueck
authors.affiliation: Department of Pharmacology, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
authors.forename: Tae Kyung
authors.initials: TK
authors.lastname: Kim
authors.affiliation: Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
authors.forename: Stephen
authors.initials: S
authors.lastname: Fisher
authors.affiliation: Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
authors.forename: Chantal
authors.initials: C
authors.lastname: Francis
authors.affiliation: Department of Pharmacology, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
authors.forename: Jennifer M
authors.initials: JM
authors.lastname: Spaethling
authors.affiliation: Department of Neurosurgery, University of Pennsylvania Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
authors.forename: John A
authors.initials: JA
authors.lastname: Wolf
authors.affiliation: Department of Neurosurgery, University of Pennsylvania Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
authors.forename: M Sean
authors.initials: MS
authors.lastname: Grady
authors.affiliation: Department of Neurosurgery, University of Pennsylvania Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
authors.forename: Alexandra V
authors.initials: AV
authors.lastname: Ulyanova
authors.affiliation: Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
authors.forename: Sean B
authors.initials: SB
authors.lastname: Yeldell
authors.affiliation: Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
authors.forename: Julianne C
authors.initials: JC
authors.lastname: Griepenburg
authors.affiliation: Department of Pharmacology, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
authors.forename: Peter T
authors.initials: PT
authors.lastname: Buckley
authors.affiliation: 1] Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA. [2] PENN Genome Frontiers Institute, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
authors.forename: Junhyong
authors.initials: J
authors.lastname: Kim
authors.affiliation: Department of Pharmacology, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
authors.forename: Jai-Yoon
authors.initials: JY
authors.lastname: Sul
authors.affiliation: 1] Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA. [2].
authors.forename: Ivan J
authors.initials: IJ
authors.lastname: Dmochowski
authors.affiliation: 1] Department of Pharmacology, University of Pennsylvania, Philadelphia, Pennsylvania, USA. [2] PENN Genome Frontiers Institute, University of Pennsylvania, Philadelphia, Pennsylvania, USA. [3].
authors.forename: James
authors.initials: J
authors.lastname: Eberwine
mesh_terms: D000818:Animals; D001921:Brain / Q000378:metabolism*; D019295:Computational Biology; D020869:Gene Expression Profiling; D015723:Gene Library; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006624:Hippocampus / Q000378:metabolism*; D006801:Humans; D051379:Mice; D008810:Mice, Inbred C57BL; D009474:Neurons / Q000378:metabolism*; D012333:RNA, Messenger / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D012333:RNA, Messenger