Advancing root developmental research through single-cell technologies

2022 ◽  
Vol 65 ◽  
pp. 102113
Author(s):  
Max Minne ◽  
Yuji Ke ◽  
Maite Saura-Sanchez ◽  
Bert De Rybel
Cell Systems ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 388-400
Author(s):  
Maeve P. Nagle ◽  
Gabriela S. Tam ◽  
Evan Maltz ◽  
Zachary Hemminger ◽  
Roy Wollman

2022 ◽  
Vol 8 ◽  
Author(s):  
Eric Schoger ◽  
Sara Lelek ◽  
Daniela Panáková ◽  
Laura Cecilia Zelarayán

Molecular and genetic differences between individual cells within tissues underlie cellular heterogeneities defining organ physiology and function in homeostasis as well as in disease states. Transcriptional control of endogenous gene expression has been intensively studied for decades. Thanks to a fast-developing field of single cell genomics, we are facing an unprecedented leap in information available pertaining organ biology offering a comprehensive overview. The single-cell technologies that arose aided in resolving the precise cellular composition of many organ systems in the past years. Importantly, when applied to diseased tissues, the novel approaches have been immensely improving our understanding of the underlying pathophysiology of common human diseases. With this information, precise prediction of regulatory elements controlling gene expression upon perturbations in a given cell type or a specific context will be realistic. Simultaneously, the technological advances in CRISPR-mediated regulation of gene transcription as well as their application in the context of epigenome modulation, have opened up novel avenues for targeted therapy and personalized medicine. Here, we discuss the fast-paced advancements during the recent years and the applications thereof in the context of cardiac biology and common cardiac disease. The combination of single cell technologies and the deep knowledge of fundamental biology of the diseased heart together with the CRISPR-mediated modulation of gene regulatory networks will be instrumental in tailoring the right strategies for personalized and precision medicine in the near future. In this review, we provide a brief overview of how single cell transcriptomics has advanced our knowledge and paved the way for emerging CRISPR/Cas9-technologies in clinical applications in cardiac biomedicine.


2021 ◽  
pp. 15-30
Author(s):  
Nigel Kee ◽  
Maria Papathanou

2019 ◽  
Vol 82 (3) ◽  
Author(s):  
Jessica Vazquez ◽  
Irene M. Ong ◽  
Aleksandar K. Stanic

2017 ◽  
Vol 7 ◽  
Author(s):  
Brant Hubbard

2014 ◽  
Vol 15 (2) ◽  
pp. 128-135 ◽  
Author(s):  
Pratip K Chattopadhyay ◽  
Todd M Gierahn ◽  
Mario Roederer ◽  
J Christopher Love

2019 ◽  
Author(s):  
Hannah A. Pliner ◽  
Jay Shendure ◽  
Cole Trapnell

ABSTRACTSingle cell technologies for profiling tissues or even entire organisms are rapidly being adopted. However, the manual process by which cell types are typically annotated in the resulting data is labor-intensive and increasingly rate-limiting for the field. Here we describe Garnett, an algorithm and accompanying software for rapidly annotating cell types in scRNA-seq and scATAC-seq datasets, based on an interpretable, hierarchical markup language of cell type-specific genes. Garnett successfully classifies cell types in tissue and whole organism datasets, as well as across species.


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