Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis

Farrell, Jeffrey A.; Wang, Yiqun; Riesenfeld, Samantha J.; Shekhar, Karthik; Regev, Aviv; Schier, Alexander F.

doi:10.1126/science.aar3131

Cited by 703 publications

(838 citation statements)

References 48 publications

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“…However, these methods alone do not track cell dynamics that influence tissue structure, such as timing and location of cell divisions [34-36]. Furthermore, as we show in this study, cell death is common in growth and regeneration, and retrospective cell sequencing excludes cells that do not survive to the point of cell harvest.…”

Section: Discussionmentioning

confidence: 93%

In Toto Imaging of Dynamic Osteoblast Behaviors in Regenerating Skeletal Bone

et al. 2018

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SUMMARY Osteoblasts are matrix-depositing cells that can divide and heal bone injuries. Their deep tissue location and the slow progression of bone regeneration challenge attempts to capture osteoblast behaviors in live tissue at high spatiotemporal resolution. Here, we have developed an imaging platform to monitor and quantify individual and collective behaviors of osteoblasts in adult zebrafish scales, skeletal body armor discs that regenerate rapidly after loss. Using a panel of transgenic lines that visualize and manipulate osteoblasts, we find that a founder pool of osteoblasts emerges through de novo differentiation within one day of scale plucking. These osteoblasts undergo division events that are largely uniform in frequency and orientation to establish a primordium. Osteoblast proliferation dynamics diversify across the primordium by two days after injury, with cell divisions focused near, and with orientations parallel to, the scale periphery, occurring coincident with dynamic localization of fgf20a gene expression. In posterior scale regions, cell elongation events initiate in areas soon occupied by mineralized grooves called radii, beginning approximately 2 days postinjury, with patterned osteoblast death events accompanying maturation of these radii. By imaging at single-cell resolution, we detail acquisition of spatiotemporally distinct cell division, motility, and death dynamics within a founder osteoblast pool as bone regenerates.

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Section: Discussionmentioning

confidence: 93%

In Toto Imaging of Dynamic Osteoblast Behaviors in Regenerating Skeletal Bone

et al. 2018

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“…Moreover, computational methods exist to determine the lineage relationship of individual cells within a scRNAseq data set, as well as to discover rare cell populations. 73,80,81 These tools, together with the ability to complement computational studies with informed genetic lineage-tracing and knockout studies in mice, will provide valuable insight into the question of cell plasticity and lineage restriction in mouse digit tip regeneration.…”

Section: Cell Plasticity Versus Lineage Restriction During Digit Tipmentioning

confidence: 99%

Cellular Plasticity in Musculoskeletal Development, Regeneration, and Disease

Kaji

Tan

Johnson

et al. 2019

Journal Orthopaedic Research

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In this review, we highlight themes from a recent workshop focused on “Plasticity of Cell Fate in Musculoskeletal Tissues” held at the Orthopaedic Research Society's 2019 annual meeting. Experts in the field provided examples of mesenchymal cell plasticity during normal musculoskeletal development, regeneration, and disease. A thorough understanding of the biology underpinning mesenchymal cell plasticity may offer a roadmap for promoting regeneration while attenuating pathologic differentiation. © 2019 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 38:708‐718, 2020

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“…The main cerebellar lineages were identified to uncover the engine behind these processes at different branching points, which enhanced the knowledge of neurodevelopment . Similar technologies were also applied to investigate the differentiation and growth dynamics of other species, such as Zebrafish, Xenopus laevis , and Arabidopsis, etc.…”

Section: Applicationsmentioning

confidence: 99%

Microfluidic Single‐Cell Omics Analysis

Wang

et al. 2019

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The commonly existing cellular heterogeneity plays a critical role in biological processes such as embryonic development, cell differentiation, and disease progress. Single‐cell omics‐based heterogeneous studies have great significance for identifying different cell populations, discovering new cell types, revealing informative cell features, and uncovering significant interrelationships between cells. Recently, microfluidics has evolved to be a powerful technology for single‐cell omics analysis due to its merits of throughput, sensitivity, and accuracy. Herein, the recent advances of microfluidic single‐cell omics analysis, including different microfluidic platform designs, lysis strategies, and omics analysis techniques, are reviewed. Representative applications of microfluidic single‐cell omics analysis in complex biological studies are then summarized. Finally, a few perspectives on the future challenges and development trends of microfluidic‐assisted single‐cell omics analysis are discussed.

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Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis

Cited by 703 publications

References 48 publications

In Toto Imaging of Dynamic Osteoblast Behaviors in Regenerating Skeletal Bone

In Toto Imaging of Dynamic Osteoblast Behaviors in Regenerating Skeletal Bone

Cellular Plasticity in Musculoskeletal Development, Regeneration, and Disease

Microfluidic Single‐Cell Omics Analysis

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