Comprehensive single-cell transcriptional profiling of a multicellular organism

Junyue Cao, Jonathan S. Packer, Vijay Ramani, Darren A. Cusanovich, Chau Huynh, Riza Daza, Xiaojie Qiu, Choli Lee, Scott N. Furlan, Frank J. Steemers, Andrew Adey, Robert H. Waterston, Cole Trapnell, Jay Shendure

Research output: Contribution to journalArticle

143 Citations (Scopus)

Abstract

To resolve cellular heterogeneity, we developed a combinatorial indexing strategy to profile the transcriptomes of single cells or nuclei, termed sci-RNA-seq (single-cell combinatorial indexing RNA sequencing). We applied sci-RNA-seq to profile nearly 50,000 cells from the nematode Caenorhabditis elegans at the L2 larval stage, which provided >50-fold “shotgun” cellular coverage of its somatic cell composition. From these data, we defined consensus expression profiles for 27 cell types and recovered rare neuronal cell types corresponding to as few as one or two cells in the L2 worm. We integrated these profiles with whole-animal chromatin immunoprecipitation sequencing data to deconvolve the cell type–specific effects of transcription factors. The data generated by sci-RNA-seq constitute a powerful resource for nematode biology and foreshadow similar atlases for other organisms.

Original languageEnglish (US)
Pages (from-to)661-667
Number of pages7
JournalScience
Volume357
Issue number6352
DOIs
StatePublished - Aug 18 2017

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RNA Sequence Analysis
Atlases
Chromatin Immunoprecipitation
Caenorhabditis elegans
Firearms
Cell Nucleus
Transcriptome
Transcription Factors

ASJC Scopus subject areas

  • Medicine(all)
  • General

Cite this

Cao, J., Packer, J. S., Ramani, V., Cusanovich, D. A., Huynh, C., Daza, R., ... Shendure, J. (2017). Comprehensive single-cell transcriptional profiling of a multicellular organism. Science, 357(6352), 661-667. https://doi.org/10.1126/science.aam8940

Comprehensive single-cell transcriptional profiling of a multicellular organism. / Cao, Junyue; Packer, Jonathan S.; Ramani, Vijay; Cusanovich, Darren A.; Huynh, Chau; Daza, Riza; Qiu, Xiaojie; Lee, Choli; Furlan, Scott N.; Steemers, Frank J.; Adey, Andrew; Waterston, Robert H.; Trapnell, Cole; Shendure, Jay.

In: Science, Vol. 357, No. 6352, 18.08.2017, p. 661-667.

Research output: Contribution to journalArticle

Cao, J, Packer, JS, Ramani, V, Cusanovich, DA, Huynh, C, Daza, R, Qiu, X, Lee, C, Furlan, SN, Steemers, FJ, Adey, A, Waterston, RH, Trapnell, C & Shendure, J 2017, 'Comprehensive single-cell transcriptional profiling of a multicellular organism', Science, vol. 357, no. 6352, pp. 661-667. https://doi.org/10.1126/science.aam8940
Cao J, Packer JS, Ramani V, Cusanovich DA, Huynh C, Daza R et al. Comprehensive single-cell transcriptional profiling of a multicellular organism. Science. 2017 Aug 18;357(6352):661-667. https://doi.org/10.1126/science.aam8940
Cao, Junyue ; Packer, Jonathan S. ; Ramani, Vijay ; Cusanovich, Darren A. ; Huynh, Chau ; Daza, Riza ; Qiu, Xiaojie ; Lee, Choli ; Furlan, Scott N. ; Steemers, Frank J. ; Adey, Andrew ; Waterston, Robert H. ; Trapnell, Cole ; Shendure, Jay. / Comprehensive single-cell transcriptional profiling of a multicellular organism. In: Science. 2017 ; Vol. 357, No. 6352. pp. 661-667.
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