title: Highly multiplexed subcellular RNA sequencing in situ.
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.
authors.affiliation: Wyss Institute, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Je Hyuk
authors.initials: JH
authors.lastname: Lee
authors.forename: Evan R
authors.initials: ER
authors.lastname: Daugharthy
authors.forename: Jonathan
authors.initials: J
authors.lastname: Scheiman
authors.forename: Reza
authors.initials: R
authors.lastname: Kalhor
authors.forename: Joyce L
authors.initials: JL
authors.lastname: Yang
authors.forename: Thomas C
authors.initials: TC
authors.lastname: Ferrante
authors.forename: Richard
authors.initials: R
authors.lastname: Terry
authors.forename: Sauveur S F
authors.initials: SS
authors.lastname: Jeanty
authors.forename: Chao
authors.initials: C
authors.lastname: Li
authors.forename: Ryoji
authors.initials: R
authors.lastname: Amamoto
authors.forename: Derek T
authors.initials: DT
authors.lastname: Peters
authors.forename: Brian M
authors.initials: BM
authors.lastname: Turczyk
authors.forename: Adam H
authors.initials: AH
authors.lastname: Marblestone
authors.forename: Samuel A
authors.initials: SA
authors.lastname: Inverso
authors.forename: Amy
authors.initials: A
authors.lastname: Bernard
authors.forename: Prashant
authors.initials: P
authors.lastname: Mali
authors.forename: Xavier
authors.initials: X
authors.lastname: Rios
authors.forename: John
authors.initials: J
authors.lastname: Aach
authors.forename: George M
authors.initials: GM
authors.lastname: Church
mesh_terms: D001483:Base Sequence; D002460:Cell Line; D002478:Cells, Cultured; D018076:DNA, Complementary; D005453:Fluorescence; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D057026:Induced Pluripotent Stem Cells; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA / Q000379:methods*; D059010:Single-Cell Analysis; D024363:Transcription Initiation Site; D059467:Transcriptome; D014945:Wound Healing
chemical_list: D018076:DNA, Complementary; D012333:RNA, Messenger