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A single-cell time-lapse of mouse prenatal development from gastrula to birth.

ABSTRACT: The house mouse (Mus musculus) is an exceptional model system, combining genetic tractability with close evolutionary affinity to humans^1,2. Mouse gestation lasts only 3 weeks, during which the genome orchestrates the astonishing transformation of a single-cell zygote into a free-living pup composed of more than 500 million cells. Here, to establish a global framework for exploring mammalian development, we applied optimized single-cell combinatorial indexing³ to profile the transcriptional states of 12.4 million nuclei from 83 embryos, precisely staged at 2- to 6-hour intervals spanning late gastrulation (embryonic day 8) to birth (postnatal day 0). From these data, we annotate hundreds of cell types and explore the ontogenesis of the posterior embryo during somitogenesis and of kidney, mesenchyme, retina and early neurons. We leverage the temporal resolution and sampling depth of these whole-embryo snapshots, together with published data^4-8 from earlier timepoints, to construct a rooted tree of cell-type relationships that spans the entirety of prenatal development, from zygote to birth. Throughout this tree, we systematically nominate genes encoding transcription factors and other proteins as candidate drivers of the in vivo differentiation of hundreds of cell types. Remarkably, the most marked temporal shifts in cell states are observed within one hour of birth and presumably underlie the massive physiological adaptations that must accompany the successful transition of a mammalian fetus to life outside the womb.

SUBMITTER: Qiu C

PROVIDER: S-EPMC10901739 | biostudies-literature | 2024 Feb

REPOSITORIES: biostudies-literature

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A single-cell time-lapse of mouse prenatal development from gastrula to birth.

Qiu Chengxiang C Martin Beth K BK Welsh Ian C IC Daza Riza M RM Le Truc-Mai TM Huang Xingfan X Nichols Eva K EK Taylor Megan L ML Fulton Olivia O O'Day Diana R DR Gomes Anne Roshella AR Ilcisin Saskia S Srivatsan Sanjay S Deng Xinxian X Disteche Christine M CM Noble William Stafford WS Hamazaki Nobuhiko N Moens Cecilia B CB Kimelman David D Cao Junyue J Schier Alexander F AF Spielmann Malte M Murray Stephen A SA Trapnell Cole C Shendure Jay J

Nature 20240214 8001

The house mouse (Mus musculus) is an exceptional model system, combining genetic tractability with close evolutionary affinity to humans<sup>1,2</sup>. Mouse gestation lasts only 3 weeks, during which the genome orchestrates the astonishing transformation of a single-cell zygote into a free-living pup composed of more than 500 million cells. Here, to establish a global framework for exploring mammalian development, we applied optimized single-cell combinatorial indexing<sup>3</sup> to profile th ...[more]

PMID: 38355799

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Project description:The physiological heterogeneity of cells within a microbial population imparts resilience to stresses such as antimicrobial treatments and nutrient limitation. This resilience is partially due to a subpopulation of cells that can survive such stresses and regenerate the community. Microfluidic approaches now provide a means to study microbial physiology and bacterial heterogeneity at the single cell level, improving our ability to isolate and examine these subpopulations. Drop-based microfluidics provides a high-throughput approach to study individual cell physiology within bacterial populations. Using this approach, single cells are isolated from the population and encapsulated in growth medium dispersed in oil using a 15 μm diameter drop making microfluidic device. The drops are arranged as a packed monolayer inside a polydimethylsiloxane (PDMS) microfluidic device. Growth of thousands of individual cells in identical microenvironments can then be imaged using confocal laser scanning microscopy (CLSM). A challenge for this approach has been the maintenance of drop stability during extended time-lapse imaging. In particular, the drops do not maintain their volume over time during incubation in PDMS devices, due to fluid transport into the porous PDMS surroundings. Here, we present a strategy for PDMS device preparation that stabilizes drop position and volume within a drop array on a microfluidic chip for over 20 h. The stability of water-in-oil drops is maintained by soaking the device in a reservoir containing both water and oil in thermodynamic equilibrium. This ensures that phase equilibrium of the drop emulsion fluids within the porous PDMS material is maintained during drop incubation and imaging. We demonstrate the utility of this approach, which we label DropSOAC (Drop Stabilization On A Chip), for time-lapse studies of bacterial growth. We characterize growth of Pseudomonas aeruginosa and its Δhpf mutant derivative during resuscitation and growth following starvation. We demonstrate that growth rate and lag time heterogeneity of hundreds of individual bacterial cells can be determined starting from single isolated cells. The results show that the DropSOAC capsule provides a high-throughput approach toward studies of microbial physiology at the single cell level, and can be used to characterize physiological differences of cells from within a larger population.

Dataset Information

A single-cell time-lapse of mouse prenatal development from gastrula to birth.

Publications

A single-cell time-lapse of mouse prenatal development from gastrula to birth.

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