Highly multiplexed subcellular RNA sequencing in situ.

IF: 63.714

Cited by: 751

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.

Keywords

FISSEQ

Spatial Gene Expression

MeSH terms

Base Sequence

Cell Line

Cells, Cultured

DNA, Complementary

Fluorescence

Gene Expression Profiling

Humans

Induced Pluripotent Stem Cells

RNA, Messenger

Sequence Analysis, RNA

Single-Cell Analysis

Transcription Initiation Site

Transcriptome

Wound Healing

Authors

Lee, Je Hyuk

Daugharthy, Evan R

Scheiman, Jonathan

Kalhor, Reza

Yang, Joyce L

Ferrante, Thomas C

Terry, Richard

Jeanty, Sauveur S F

Li, Chao

Amamoto, Ryoji

Peters, Derek T

Turczyk, Brian M

Marblestone, Adam H

Inverso, Samuel A

Bernard, Amy

Mali, Prashant

Rios, Xavier

Aach, John

Church, George M

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