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Nat Biotechnol. 2018 Jun;36(5):442-450. doi: 10.1038/nbt.4103. Epub 2018 Mar 28.

Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain.

Raj B1,2, Wagner DE3, McKenna A2,4, Pandey S1, Klein AM3, Shendure J2,4,5, Gagnon JA1,2,6, Schier AF1,2,7,8,9,10.

Author information

1
Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA.
2
Allen Discovery Center for Cell Lineage Tracing, Seattle, Washington, USA.
3
Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA.
4
Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
5
Howard Hughes Medical Institute, Seattle, Washington, USA.
6
Department of Biology, University of Utah, Salt Lake City, Utah, USA.
7
Biozentrum, University of Basel, Switzerland.
8
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
9
Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts, USA.
10
Center for Brain Science, Harvard University, Cambridge, Massachusetts, USA.

Abstract

The lineage relationships among the hundreds of cell types generated during development are difficult to reconstruct. A recent method, GESTALT, used CRISPR-Cas9 barcode editing for large-scale lineage tracing, but was restricted to early development and did not identify cell types. Here we present scGESTALT, which combines the lineage recording capabilities of GESTALT with cell-type identification by single-cell RNA sequencing. The method relies on an inducible system that enables barcodes to be edited at multiple time points, capturing lineage information from later stages of development. Sequencing of ∼60,000 transcriptomes from the juvenile zebrafish brain identified >100 cell types and marker genes. Using these data, we generate lineage trees with hundreds of branches that help uncover restrictions at the level of cell types, brain regions, and gene expression cascades during differentiation. scGESTALT can be applied to other multicellular organisms to simultaneously characterize molecular identities and lineage histories of thousands of cells during development and disease.

Comment in

PMID:
29608178
PMCID:
PMC5938111
DOI:
10.1038/nbt.4103
[Indexed for MEDLINE]
Free PMC Article

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