Charting human development using a multi-endodermal organ atlas and organoid models
Qianhui Yu,Umut Kilik,Emily M. Holloway,Yu-Hwai Tsai,Christoph Harmel,Angeline Wu,Joshua H. Wu,Michael Czerwinski,Charlie Childs,Zhisong He,Meghan M. Capeling,Sha Huang,Ian A. Glass,Peter D.R. Higgins,Barbara Treutlein,Jason R. Spence,J. Gray Camp +16 more
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TLDR
This work generates a single-cell transcriptome atlas from multiple developing endodermal organs of the respiratory and gastrointestinal tract and implements the atlas as a high-dimensional search space to benchmark human pluripotent stem cell (hPSC)-derived intestinal organoids (HIOs) under multiple culture conditions.About:
This article is published in Cell.The article was published on 2021-06-10 and is currently open access. It has received 53 citations till now. The article focuses on the topics: Induced pluripotent stem cell & Mesenchyme.read more
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Human organoids: New strategies and methods for analyzing human development and disease
TL;DR: A review of advances in organoid biology with a focus on how organoid technology has generated a better understanding of human-specific processes in development and disease can be found in this paper .
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Generation and characterization of hair-bearing skin organoids from human pluripotent stem cells
Jiyoon Lee,Wouter H van der Valk,Sara A. Serdy,CiCi Deakin,Jin Kim,Anh Phuong Le,Karl R. Koehler +6 more
TL;DR: In this article , a detailed protocol for generating hair-bearing skin tissue entirely from a homogeneous population of human pluripotent stem cells in a three-dimensional in vitro culture system is described.
Journal ArticleDOI
Stable iPSC-derived NKX2-1+ lung bud tip progenitor organoids give rise to airway and alveolar cell types
R. Hein,Ansley S. Conchola,Alexis Fine,Zhiwei Xiao,Tristan Frum,Charlie Childs,Yu Hwai Tsai,Emily M. Holloway,Sha Huang,John E. Mahoney,Jason R. Spence +10 more
TL;DR: iPSC-derived lung bud tip progenitors emerge in organoid culture, can be isolated and expanded, are transcriptionally similar to primary bud tip PROGenitors, and can differentiate into airway or alveolar organoids.
Journal ArticleDOI
A reference single-cell regulomic and transcriptomic map of cynomolgus monkeys
Jiao Qu,Farhana SaC Yang,Tao Zhu,Yingshuo Wang,Wen Fang,Yan Ding,Xue Zhao,Xianjia Qi,Qiang-min Xie,Qiang Xu,Yicheng Xie,Yang Sun,Dijun Chen +12 more
TL;DR: In this article , a compendium of cell types across multiple organs in cynomolgus monkeys ( Macaca fascicularis ) using both single-cell chromatin accessibility and RNA sequencing data is presented.
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Source and Impact of the EGF Family of Ligands on Intestinal Stem Cells.
TL;DR: The role of EGF in the development of intestinal stem cells through the ErbB pathway is investigated in this paper, where the authors identify diverse stromal cell populations that reside underneath intestinal crypts and characterize key growth factor cues supplied by these cells.
References
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Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
Aravind Subramanian,Pablo Tamayo,Vamsi K. Mootha,Sayan Mukherjee,Benjamin L. Ebert,Michael A. Gillette,Amanda G. Paulovich,Scott L. Pomeroy,Todd R. Golub,Eric S. Lander,Jill P. Mesirov +10 more
TL;DR: The Gene Set Enrichment Analysis (GSEA) method as discussed by the authors focuses on gene sets, that is, groups of genes that share common biological function, chromosomal location, or regulation.
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Integrating single-cell transcriptomic data across different conditions, technologies, and species.
TL;DR: An analytical strategy for integrating scRNA-seq data sets based on common sources of variation is introduced, enabling the identification of shared populations across data sets and downstream comparative analysis.
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Identification of stem cells in small intestine and colon by marker gene Lgr5
Nick Barker,Johan H. van Es,Jeroen Kuipers,Pekka Kujala,Maaike van den Born,Miranda Cozijnsen,Andrea Haegebarth,Jeroen Korving,Harry Begthel,Peter J. Peters,Hans Clevers +10 more
TL;DR: The expression pattern of Lgr5 suggests that it marks stem cells in multiple adult tissues and cancers, suggesting that it represents the stem cell of the small intestine and colon.
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Molecular signatures database (MSigDB) 3.0
Arthur Liberzon,Aravind Subramanian,Reid M. Pinchback,Helga Thorvaldsdottir,Pablo Tamayo,Jill P. Mesirov +5 more
TL;DR: A new version of the database, MSigDB 3.0, is reported, with over 6700 gene sets, a complete revision of the collection of canonical pathways and experimental signatures from publications, enhanced annotations and upgrades to the web site.
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Dimensionality reduction for visualizing single-cell data using UMAP.
Etienne Becht,Leland McInnes,John Healy,Charles-Antoine Dutertre,Immanuel Kwok,Lai Guan Ng,Florent Ginhoux,Evan W. Newell,Evan W. Newell +8 more
TL;DR: Comparing the performance of UMAP with five other tools, it is found that UMAP provides the fastest run times, highest reproducibility and the most meaningful organization of cell clusters.
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