A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution
Jonathan S. Packer,Qin Zhu,Chau Huynh,Priya Sivaramakrishnan,Elicia Preston,Hannah Dueck,Derek Stefanik,Kai Tan,Cole Trapnell,Junhyong Kim,Robert H. Waterston,John I. Murray +11 more
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TLDR
The dataset defines the succession of gene expression changes associated with almost every cell division in an animal's embryonic cell lineage, and provides an extensive resource that will guide future investigations of gene regulation and cell fate decisions in C. elegans.Abstract:
Caenorhabditis elegans is an animal with few cells but a wide diversity of cell types. In this study, we characterize the molecular basis for their specification by profiling the transcriptomes of 86,024 single embryonic cells. We identify 502 terminal and preterminal cell types, mapping most single-cell transcriptomes to their exact position in C. elegans' invariant lineage. Using these annotations, we find that (i) the correlation between a cell's lineage and its transcriptome increases from middle to late gastrulation, then falls substantially as cells in the nervous system and pharynx adopt their terminal fates; (ii) multilineage priming contributes to the differentiation of sister cells at dozens of lineage branches; and (iii) most distinct lineages that produce the same anatomical cell type converge to a homogenous transcriptomic state.read more
Citations
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Single-cell transcriptional diversity is a hallmark of developmental potential.
Gunsagar S. Gulati,Shaheen S. Sikandar,Daniel J. Wesche,Anoop Manjunath,Anjan Bharadwaj,Mark J. Berger,Francisco Ilagan,Angera H. Kuo,Robert W. Hsieh,Shang Cai,Maider Zabala,Ferenc A. Scheeren,Neethan A. Lobo,Dalong Qian,Feiqiao Brian Yu,Frederick M. Dirbas,Michael F. Clarke,Aaron M. Newman +17 more
TL;DR: A simple, yet robust, determinant of developmental potential—the number of expressed genes per cell—is demonstrated and leverage this measure of transcriptional diversity to develop a computational framework (CytoTRACE) for predicting differentiation states from scRNA-seq data.
Journal ArticleDOI
Lineage tracing meets single-cell omics: opportunities and challenges.
Daniel E. Wagner,Allon M. Klein +1 more
TL;DR: Progress in modern lineage-tracing methods that combine genetic lineage analysis with omics-based characterization of cell states (particularly transcriptomes) are discussed, as well as the biological insights gained.
Journal ArticleDOI
Single-Cell Profiling Reveals Sex, Lineage, and Regional Diversity in the Mouse Kidney.
Andrew Ransick,Nils O. Lindström,Jing Liu,Qin Zhu,Jinjin Guo,Gregory F. Alvarado,Albert D. Kim,Hannah G. Black,Junhyong Kim,Andrew P. McMahon +9 more
TL;DR: To enhance an understanding of the mammalian kidney, anatomy-guided single-cell RNA sequencing of the adult male and female mouse kidney is combined with in situ expression studies and cell lineage tracing to reveal cell diversity and marked sex differences.
Journal ArticleDOI
Molecular topography of an entire nervous system.
Seth R. Taylor,Gabriel Santpere,Gabriel Santpere,Alexis Weinreb,Alec Barrett,Molly B. Reilly,Molly B. Reilly,Chuan Xu,Erdem Varol,Panos Oikonomou,Panos Oikonomou,Lori Glenwinkel,Lori Glenwinkel,Rebecca McWhirter,Abigail Poff,Manasa Basavaraju,Ibnul Rafi,Ibnul Rafi,Eviatar Yemini,Eviatar Yemini,Steven J. Cook,Steven J. Cook,Alexander J. Abrams,Berta Vidal,Berta Vidal,Cyril Cros,Cyril Cros,Saeed Tavazoie,Saeed Tavazoie,Nenad Sestan,Marc Hammarlund,Oliver Hobert,Oliver Hobert,David M. Miller +33 more
TL;DR: In this paper, the authors have produced gene expression profiles of all 302 neurons of the C. elegans nervous system that match the single-cell resolution of its anatomy and wiring diagram, showing that individual neuron classes can be solely identified by combinatorial expression of specific gene families.
Posted ContentDOI
Molecular topography of an entire nervous system
Seth R. Taylor,Gabriel Santpere,Alexis Weinreb,Alec Barrett,Molly B. Reilly,Molly B. Reilly,Chuan Xu,Erdem Varol,Panos Oikonomou,Panos Oikonomou,Lori Glenwinkel,Lori Glenwinkel,Rebecca McWhirter,Abigail Poff,Manasa Basavaraju,Ibnul Rafi,Ibnul Rafi,Eviatar Yemini,Eviatar Yemini,Steven J. Cook,Steven J. Cook,Alexander J. Abrams,Berta Vidal,Berta Vidal,Cyril Cros,Cyril Cros,Saeed Tavazoie,Saeed Tavazoie,Nenad Sestan,Marc Hammarlund,Oliver Hobert,Oliver Hobert,David M. Miller +32 more
TL;DR: An expression profile of all 302 neurons of the C. elegans nervous system is produced that matches the single cell resolution of its anatomy and wiring diagram and suggests that individual neuron classes can be solely identified by combinatorial expression of specific gene families.
References
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Fast unfolding of communities in large networks
Vincent D. Blondel,Jean-Loup Guillaume,Jean-Loup Guillaume,Renaud Lambiotte,Renaud Lambiotte,Etienne Lefebvre +5 more
TL;DR: This work proposes a heuristic method that is shown to outperform all other known community detection methods in terms of computation time and the quality of the communities detected is very good, as measured by the so-called modularity.
Journal ArticleDOI
Fast unfolding of communities in large networks
Vincent D. Blondel,Jean-Loup Guillaume,Jean-Loup Guillaume,Renaud Lambiotte,Renaud Lambiotte,Etienne Lefebvre +5 more
TL;DR: In this paper, the authors proposed a simple method to extract the community structure of large networks based on modularity optimization, which is shown to outperform all other known community detection methods in terms of computation time.
Posted Content
UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction
Leland McInnes,John Healy +1 more
TL;DR: The UMAP algorithm is competitive with t-SNE for visualization quality, and arguably preserves more of the global structure with superior run time performance.
Journal ArticleDOI
UMAP: Uniform Manifold Approximation and Projection
TL;DR: Uniform Manifold Approximation and Projection (UMAP) is a dimension reduction technique that can be used for visualisation similarly to t-SNE, but also for general non-linear dimension reduction.
Journal ArticleDOI
The embryonic cell lineage of the nematode Caenorhabditis elegans.
TL;DR: It is concluded that the cell lineage itself, complex as it is, plays an important role in determining cell fate and is demonstrated to demonstrate substantial cell autonomy in at least some sections of embryogenesis.
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