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Science. 2018 Apr 13;360(6385):176-182. doi: 10.1126/science.aam8999. Epub 2018 Mar 15.

Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding.

Author information

1
Department of Electrical Engineering, University of Washington, Seattle, WA, USA. alex.b.rosenberg@gmail.com gseelig@uw.edu.
2
Department of Bioengineering, University of Washington, Seattle, WA, USA.
3
Department of Electrical Engineering, University of Washington, Seattle, WA, USA.
4
Allen Institute for Brain Science, Seattle, WA, USA.
5
Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA.
6
Institute for Stem Cell and Regenerative Medicine, Seattle, WA, USA.
7
Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA.

Abstract

To facilitate scalable profiling of single cells, we developed split-pool ligation-based transcriptome sequencing (SPLiT-seq), a single-cell RNA-seq (scRNA-seq) method that labels the cellular origin of RNA through combinatorial barcoding. SPLiT-seq is compatible with fixed cells or nuclei, allows efficient sample multiplexing, and requires no customized equipment. We used SPLiT-seq to analyze 156,049 single-nucleus transcriptomes from postnatal day 2 and 11 mouse brains and spinal cords. More than 100 cell types were identified, with gene expression patterns corresponding to cellular function, regional specificity, and stage of differentiation. Pseudotime analysis revealed transcriptional programs driving four developmental lineages, providing a snapshot of early postnatal development in the murine central nervous system. SPLiT-seq provides a path toward comprehensive single-cell transcriptomic analysis of other similarly complex multicellular systems.

PMID:
29545511
DOI:
10.1126/science.aam8999
[Indexed for MEDLINE]

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