Molecular architecture of lineage allocation and tissue organization in early mouse embryo

Nature, Год журнала: 2019, Номер 572(7770), С. 528 - 532

Опубликована: Авг. 7, 2019

Язык: Английский

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Embryo-scale, single-cell spatial transcriptomics

Science, Год журнала: 2021, Номер 373(6550), С. 111 - 117

Опубликована: Июль 1, 2021

Spatial patterns of gene expression manifest at scales ranging from local (e.g., cell-cell interactions) to global body axis patterning). However, current spatial transcriptomics methods either average contexts or are restricted limited fields view. Here, we introduce sci-Space, which retains single-cell resolution while resolving heterogeneity larger scales. Applying sci-Space developing mouse embryos, captured approximate coordinates and whole transcriptomes about 120,000 nuclei. We identify thousands genes exhibiting anatomically patterned expression, leverage information annotate cellular subtypes, show that cell types vary substantially in their extent patterning, reveal correlations between pseudotime the migratory differentiating neurons. Looking forward, anticipate will facilitate construction spatially resolved atlases mammalian development.

Язык: Английский

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Mapping single-cell atlases throughout Metazoa unravels cell type evolution

eLife, Год журнала: 2021, Номер 10

Опубликована: Май 4, 2021

Comparing single-cell transcriptomic atlases from diverse organisms can elucidate the origins of cellular diversity and assist annotation new cell atlases. Yet, comparison between distant relatives is hindered by complex gene histories diversifications in expression programs. Previously, we introduced self-assembling manifold (SAM) algorithm to robustly reconstruct manifolds data (Tarashansky et al., 2019). Here, build on SAM map atlas across species. This method, SAMap, identifies homologous types with shared programs species within phyla, even examples where tissues emerge distinct germ layers. SAMap also finds many genes more similar their paralogs than orthologs, suggesting paralog substitution may be common evolution previously appreciated. Lastly, comparing animal spanning sponge mouse, reveals ancient contractile stem families, which have arisen early evolution.

Язык: Английский

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Comprehensive single-cell transcriptome lineages of a proto-vertebrate

Nature, Год журнала: 2019, Номер 571(7765), С. 349 - 354

Опубликована: Июль 10, 2019

Язык: Английский

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Self-Organization of Mouse Stem Cells into an Extended Potential Blastoid

Developmental Cell, Год журнала: 2019, Номер 51(6), С. 698 - 712.e8

Опубликована: Дек. 1, 2019

Язык: Английский

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