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Series GSE52525 Query DataSets for GSE52525
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
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.
Overall design Samples represent cortex and hippocampus neuron cells collected by pipette and TIVA captured.
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
Department Biology
Lab Junhyong Kim
Street address 433 S University Avenue
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
Platforms (2)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (28)
GSM1268907 CTX_11
GSM1268908 CTX_7
GSM1268909 CTX_8
BioProject PRJNA229175
SRA SRP033139

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Supplementary file Size Download File type/resource
GSE52525_RAW.tar 5.2 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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