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| Status |
Public on Jan 12, 2014 |
| Title |
Transcriptome In Vivo Analysis (TIVA) of spatially defined single cells in intact live mouse and human brain tissue |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Transcriptome profiling is an indispensable tool in advancing the understanding of single cell biology, but depends upon methods capable of isolating mRNA at the spatial resolution of a single cell. Current capture methods lack sufficient spatial resolution to isolate mRNA from individual in vivo resident cells without damaging adjacent tissue. Because of this limitation, it has been difficult to assess the influence of the microenvironment on the transcriptome of individual neurons. Here, 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-seq to analyze transcriptome variance among single dispersed cells and in vivo resident mouse and human neurons, we show that the tissue microenvironment shapes the transcriptomic landscape of individual cells. The TIVA methodology provides the first noninvasive approach for capturing mRNA from single cells in their natural microenvironment.
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| Overall design |
Samples represent cortex and hippocampus neuron cells collected by pipette and TIVA captured.
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| Contributor(s) |
Lovatt D, Ruble BK, Lee J, Dueck H, Richards JL, Kim TK, Fisher S, Francis C, Spaethling JM, Wolf JA, Grady MS, Ulyanova AV, Greipenbrug JC, Buckley PT, Kim J, Sul J, Dmochowski IJ, Eberwine J |
| Citation(s) |
24412976 |
| Submission date |
Nov 19, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Junhyong Kim |
| Organization name |
University of Pennsylvania
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| Department |
Biology
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| Lab |
Junhyong Kim
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| Street address |
433 S University Avenue
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| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
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| Platforms (2) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
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| Samples (28)
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| Relations |
| BioProject |
PRJNA229175 |
| SRA |
SRP033139 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE52525_RAW.tar |
5.2 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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