Mapping vertebrate differentiation hierarchies with
high-throughput single-cell transcriptomics
Wagner DE, Megason SG, Klein AM
Department of Systems Biology, Harvard Medical School, Boston, MA
This project addresses a longstanding goal of developmental
biology: to map the detailed molecular events beginning with the expansion of
pluripotent blastomeres to the differentiation of all mature cell types in the
body. To date, many key molecular components and cell types have been
catalogued through the use of genetic screens, perturbations, and fate mapping.
However, a precise understanding of how cells choose their final identities requires
deeper examinations of transitional states in development.
Here, we use high-throughput single-cell transcriptomics to
deliver a quantitative map of early vertebrate development, using the zebrafish
as a model. Single-cell suspensions were generated from dissociated zebrafish
embryos from 7 timepoints spanning the first 24 hours post-fertilization. Over
35,000 individual cells were then encapsulated using a microfluidic
droplet-based barcoding platform (“inDrops”, Klein et al 2015) and analyzed by
single-cell RNAseq. Established dimensionality reduction and clustering
analyses revealed a comprehensive atlas of cell states, which increased in
complexity over developmental time. In total, we annotated over 194 cell states
(representing both stable cell types as well as dynamic processes) using data
from the ZFIN gene expression database. Furthermore, we developed a
quantitative strategy for inferring cell state progression over time and
constructed a cell state “tree” for development. This tree recapitulates a
branching pattern: cells initially expressing early pluripotency markers give
rise to distinct germ layers, and progressively discrete tissue-specific
compartments. In addition to providing a rich resource for gene discovery, our
data also reveal several novel cell types, and elucidate a previously unknown
lineage branching event.
Credits: None available.
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