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Rabies virus-based barcoded neuroanatomy resolved by single-cell RNA and in situ sequencing
Aixin Zhang,L.M. Jin,Shenqin Yao,Makoto Matsuyama,Cindy T. J. van Velthoven,Heather A. Sullivan,Na Sun,Manolis Kellis,Bosiljka Tasic,Ian R. Wickersham,Xiaoyin Chen +10 more
TL;DR: In this article , the authors combined barcoded rabies virus with single-cell and in situ sequencing to perform retrograde labeling and transsynaptic labeling in the mouse brain and identified long-range projecting cortical cell types from multiple cortical areas and identified cell types with converging or diverging synaptic connectivity.
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Array tomography: trails to discovery
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Rabies virus-based barcoded neuroanatomy resolved by single-cell RNA and in situ sequencing
Aixin Zhang,Lirong Jin,Shenqin Yao,Makoto Matsuyama,Cindy T. J. van Velthoven,Heather A. Sullivan,Ning Sun,M Kellis,Bosiljka Tasic,Ian R. Wickersham,Xiaoyin Chen +10 more
TL;DR: High-throughput and low-cost neuroanatomical techniques based on RNA barcode sequencing have the potential to map circuits at cellular resolution and a brain-wide scale, but existing techniques have limitations. This study demonstrates the utility of combining barcoded rabies virus with single-cell and in situ sequencing to map synaptic connectivity of neuronal types in the mouse brain.
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RNA regulation in brain function and disease 2022 (NeuroRNA): A conference report
TL;DR: NeRNA as mentioned in this paper integrates novel technologies and methods from the interface of RNA biology and neuroscience to deepen the understanding of gene expression programs and their regulation that underlies the cellular heterogeneity and physiology of the central nervous system.
Giotto Suite: a multi-scale and technology-agnostic spatial multi-omics analysis ecosystem
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TL;DR: Giotto Suite is a suite of open-source software packages that underlies a fully modular and integrated spatial data analysis toolbox that builds upon interoperable interfaces and data structures that bridge the established fields of genomics and spatial data science, thereby enabling independent developers to create custom-engineered pipelines.
References
Fiji: an open-source platform for biological-image analysis
Johannes Schindelin,Ignacio Arganda-Carreras,Erwin Frise,Verena Kaynig,Mark Longair,Tobias Pietzsch,Stephan Preibisch,Curtis Rueden,Stephan Saalfeld,Benjamin Schmid,Jean-Yves Tinevez,Daniel J. White,Volker Hartenstein,Kevin W. Eliceiri,Pavel Tomancak,Albert Cardona +15 more
TL;DR: Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis that facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system.
A Unique Microglia Type Associated with Restricting Development of Alzheimer’s Disease
Hadas Keren-Shaul,Amit Spinrad,Assaf Weiner,Assaf Weiner,Orit Matcovitch-Natan,Raz Dvir-Szternfeld,Tyler K. Ulland,Eyal David,Kuti Baruch,David Lara-Astaiso,Beáta Tóth,Shalev Itzkovitz,Marco Colonna,Michal Schwartz,Ido Amit +14 more
TL;DR: A novel microglia type associated with neurodegenerative diseases (DAM) is described and it is revealed that the DAM program is activated in a two-step process that involves downregulation of microglian checkpoints, followed by activation of a Trem2-dependent program.
4.2K
Spatially resolved, highly multiplexed RNA profiling in single cells
Kok Hao Chen,Alistair N. Boettiger,Jeffrey R. Moffitt,Siyuan Wang,Xiaowei Zhuang,Xiaowei Zhuang +5 more
TL;DR: This report reports multiplexed error-robust FISH (MERFISH), a single-molecule imaging method that allows thousands of RNA species to be imaged in single cells by using combinatorial FISH labeling with encoding schemes capable of detecting and/or correcting errors.
2.4K
Single-Cell RNA Sequencing of Microglia throughout the Mouse Lifespan and in the Injured Brain Reveals Complex Cell-State Changes.
Timothy R. Hammond,Timothy R. Hammond,Timothy R. Hammond,Connor Dufort,Lasse Dissing-Olesen,Lasse Dissing-Olesen,Lasse Dissing-Olesen,Stefanie Giera,Stefanie Giera,Adam Young,Alec Wysoker,Alec J. Walker,Alec J. Walker,Alec J. Walker,Frederick Gergits,Michael Segel,James Nemesh,Samuel E. Marsh,Samuel E. Marsh,Samuel E. Marsh,Arpiar Saunders,Arpiar Saunders,Evan Z. Macosko,Florent Ginhoux,Jinmiao Chen,Robin J.M. Franklin,Xianhua Piao,Xianhua Piao,Steven A. McCarroll,Steven A. McCarroll,Beth Stevens +30 more
TL;DR: The analysis of RNA expression patterns of more than 76,000 individual microglia in mice during development, in old age, and after brain injury uncovered at least nine transcriptionally distinct microglial states, which expressed unique sets of genes and were localized in the brain using specific markers.
1.8K
Lipid-Associated Macrophages Control Metabolic Homeostasis in a Trem2-Dependent Manner
Diego Jaitin,Lorenz Adlung,Christoph A. Thaiss,Assaf Weiner,Baoguo Li,Hélène Descamps,Patrick Lundgren,Camille Blériot,Zhaoyuan Liu,Aleksandra Deczkowska,Hadas Keren-Shaul,Eyal David,Niv Zmora,Shai Meron Eldar,Nir Lubezky,Oren Shibolet,David A. Hill,David A. Hill,Mitchell A. Lazar,Marco Colonna,Florent Ginhoux,Florent Ginhoux,Hagit Shapiro,Eran Elinav,Ido Amit +24 more
TL;DR: These findings identify Trem2 signaling as a major pathway by which macrophages respond to loss of tissue-level lipid homeostasis, highlighting Trem2 as a key sensor of metabolic pathologies across multiple tissues and a potential therapeutic target in metabolic diseases.
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