Highly multiplexed subcellular RNA sequencing in situ

Lee, J. H., Daugharthy, E. R., Scheiman, J., Kalhor, R., Yang, J. L., Ferrante, T. C., Terry, R., Jeanty, S. S., Li, C., Amamoto, R., Peters, D. T., Turczyk, B. M., Marblestone, A. H., Inverso, S. A., Bernard, A., Mali, P., Rios, X., Aach, J., Church, G. M. (March 2014) Highly multiplexed subcellular RNA sequencing in situ. Science, 343 (6177). pp. 1360-3. ISSN 1095-9203 (Electronic)0036-8075 (Linking)

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Abstract

Understanding the spatial organization of gene expression with single-nucleotide resolution requires localizing the sequences of expressed RNA transcripts within a cell in situ. Here, we describe fluorescent in situ RNA sequencing (FISSEQ), in which stably cross-linked complementary DNA (cDNA) amplicons are sequenced within a biological sample. Using 30-base reads from 8102 genes in situ, we examined RNA expression and localization in human primary fibroblasts with a simulated wound-healing assay. FISSEQ is compatible with tissue sections and whole-mount embryos and reduces the limitations of optical resolution and noisy signals on single-molecule detection. Our platform enables massively parallel detection of genetic elements, including gene transcripts and molecular barcodes, and can be used to investigate cellular phenotype, gene regulation, and environment in situ.

Item Type:	Paper
Uncontrolled Keywords:	Base Sequence Cell Line Cells, Cultured DNA, Complementary Fluorescence Gene Expression Profiling/ methods Humans Induced Pluripotent Stem Cells RNA, Messenger/genetics/metabolism Sequence Analysis, RNA/ methods Single-Cell Analysis Transcription Initiation Site Transcriptome Wound Healing
Subjects:	bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > transcription bioinformatics > genomics and proteomics > genetics & nucleic acid processing Investigative techniques and equipment bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > mRNA bioinformatics > genomics and proteomics > genetics & nucleic acid processing > transcriptomes
CSHL Authors:	Lee, Je Hyuk
Communities:	CSHL labs > Lee lab
Depositing User:	Matt Covey
Date:	21 March 2014
Date Deposited:	22 Jul 2015 15:21
Last Modified:	02 Oct 2019 15:05
PMCID:	PMC4140943
Related URLs:	Publisher
URI:	https://repository.cshl.edu/id/eprint/31634

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