Highly multiplexed subcellular RNA sequencing in situ

Je Hyuk Lee, Evan R. Daugharthy, Jonathan Scheiman, Reza Kalhor, Joyce L. Yang, Thomas C. Ferrante, Richard Terry, Sauveur S.F. Jeanty, Chao Li, Ryoji Amamoto, Derek T. Peters, Brian M. Turczyk, Adam H. Marblestone, Samuel A. Inverso, Amy Bernard, Prashant Mali, Xavier Rios, John Aach, George M. Church

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish (US)
Pages (from-to)1360-1363
Number of pages4
JournalScience
Volume343
Issue number6177
DOIs
StatePublished - 2014
Externally publishedYes

ASJC Scopus subject areas

  • General

Fingerprint Dive into the research topics of 'Highly multiplexed subcellular RNA sequencing in situ'. Together they form a unique fingerprint.

Cite this