Literature DB >> 32679535

Lessons from single cell sequencing in CNS cell specification and function.

Zhen Li1, William A Tyler2, Tarik F Haydar3.   

Abstract

Modern RNA sequencing methods have greatly increased our understanding of the molecular fingerprint of neurons, astrocytes and oligodendrocytes throughout the central nervous system (CNS). Technical approaches with greater sensitivity and throughput have uncovered new connections between gene expression, cell biology, and ultimately CNS function. In recent years, single cell RNA-sequencing (scRNA-seq) has made a large impact on the neurosciences by enhancing the resolution of types of cells that make up the CNS and shedding light on their developmental trajectories and how their diversity is modified across species. Here we will review the advantages, innovations, and challenges of the single cell genomics era and highlight how it has impacted our understanding of neurodevelopment and neurological function.
Copyright © 2020 Elsevier Ltd. All rights reserved.

Mesh:

Year:  2020        PMID: 32679535      PMCID: PMC7749065          DOI: 10.1016/j.gde.2020.05.043

Source DB:  PubMed          Journal:  Curr Opin Genet Dev        ISSN: 0959-437X            Impact factor:   5.578


  64 in total

1.  A comparison of single-cell trajectory inference methods.

Authors:  Wouter Saelens; Robrecht Cannoodt; Helena Todorov; Yvan Saeys
Journal:  Nat Biotechnol       Date:  2019-04-01       Impact factor: 54.908

2.  Visualization and analysis of gene expression in tissue sections by spatial transcriptomics.

Authors:  Patrik L Ståhl; Fredrik Salmén; Sanja Vickovic; Anna Lundmark; José Fernández Navarro; Jens Magnusson; Stefania Giacomello; Michaela Asp; Jakub O Westholm; Mikael Huss; Annelie Mollbrink; Sten Linnarsson; Simone Codeluppi; Åke Borg; Fredrik Pontén; Paul Igor Costea; Pelin Sahlén; Jan Mulder; Olaf Bergmann; Joakim Lundeberg; Jonas Frisén
Journal:  Science       Date:  2016-07-01       Impact factor: 47.728

Review 3.  Single cell transcriptomics in neuroscience: cell classification and beyond.

Authors:  Bosiljka Tasic
Journal:  Curr Opin Neurobiol       Date:  2018-05-05       Impact factor: 6.627

4.  Spatially Resolved Transcriptomics Enables Dissection of Genetic Heterogeneity in Stage III Cutaneous Malignant Melanoma.

Authors:  Kim Thrane; Hanna Eriksson; Jonas Maaskola; Johan Hansson; Joakim Lundeberg
Journal:  Cancer Res       Date:  2018-08-28       Impact factor: 12.701

5.  Transformation of the Radial Glia Scaffold Demarcates Two Stages of Human Cerebral Cortex Development.

Authors:  Tomasz J Nowakowski; Alex A Pollen; Carmen Sandoval-Espinosa; Arnold R Kriegstein
Journal:  Neuron       Date:  2016-09-21       Impact factor: 17.173

6.  Highly multiplexed and strand-specific single-cell RNA 5' end sequencing.

Authors:  Saiful Islam; Una Kjällquist; Annalena Moliner; Pawel Zajac; Jian-Bing Fan; Peter Lönnerberg; Sten Linnarsson
Journal:  Nat Protoc       Date:  2012-04-05       Impact factor: 13.491

7.  Massively parallel single-nucleus RNA-seq with DroNc-seq.

Authors:  Naomi Habib; Inbal Avraham-Davidi; Anindita Basu; Tyler Burks; Karthik Shekhar; Matan Hofree; Sourav R Choudhury; François Aguet; Ellen Gelfand; Kristin Ardlie; David A Weitz; Orit Rozenblatt-Rosen; Feng Zhang; Aviv Regev
Journal:  Nat Methods       Date:  2017-08-28       Impact factor: 28.547

8.  Embryonic progenitor pools generate diversity in fine-scale excitatory cortical subnetworks.

Authors:  Tommas J Ellender; Sophie V Avery; Kashif Mahfooz; Jakub Scaber; Alexander von Klemperer; Sophie L Nixon; Matthew J Buchan; Joram J van Rheede; Aleksandra Gatti; Cameron Waites; Hania J Pavlou; David Sims; Sarah E Newey; Colin J Akerman
Journal:  Nat Commun       Date:  2019-11-19       Impact factor: 14.919

9.  Conserved cell types with divergent features in human versus mouse cortex.

Authors:  Rebecca D Hodge; Trygve E Bakken; Jeremy A Miller; Kimberly A Smith; Eliza R Barkan; Lucas T Graybuck; Jennie L Close; Brian Long; Nelson Johansen; Osnat Penn; Zizhen Yao; Jeroen Eggermont; Thomas Höllt; Boaz P Levi; Soraya I Shehata; Brian Aevermann; Allison Beller; Darren Bertagnolli; Krissy Brouner; Tamara Casper; Charles Cobbs; Rachel Dalley; Nick Dee; Song-Lin Ding; Richard G Ellenbogen; Olivia Fong; Emma Garren; Jeff Goldy; Ryder P Gwinn; Daniel Hirschstein; C Dirk Keene; Mohamed Keshk; Andrew L Ko; Kanan Lathia; Ahmed Mahfouz; Zoe Maltzer; Medea McGraw; Thuc Nghi Nguyen; Julie Nyhus; Jeffrey G Ojemann; Aaron Oldre; Sheana Parry; Shannon Reynolds; Christine Rimorin; Nadiya V Shapovalova; Saroja Somasundaram; Aaron Szafer; Elliot R Thomsen; Michael Tieu; Gerald Quon; Richard H Scheuermann; Rafael Yuste; Susan M Sunkin; Boudewijn Lelieveldt; David Feng; Lydia Ng; Amy Bernard; Michael Hawrylycz; John W Phillips; Bosiljka Tasic; Hongkui Zeng; Allan R Jones; Christof Koch; Ed S Lein
Journal:  Nature       Date:  2019-08-21       Impact factor: 49.962

Review 10.  Deciphering Brain Complexity Using Single-cell Sequencing.

Authors:  Quanhua Mu; Yiyun Chen; Jiguang Wang
Journal:  Genomics Proteomics Bioinformatics       Date:  2019-10-03       Impact factor: 7.691

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  5 in total

1.  Fast and accurate matching of cellular barcodes across short-reads and long-reads of single-cell RNA-seq experiments.

Authors:  Ghazal Ebrahimi; Baraa Orabi; Meghan Robinson; Cedric Chauve; Ryan Flannigan; Faraz Hach
Journal:  iScience       Date:  2022-06-07

2.  Make war not love: The neural substrate underlying a state-dependent switch in female social behavior.

Authors:  Mengyu Liu; Dong-Wook Kim; Hongkui Zeng; David J Anderson
Journal:  Neuron       Date:  2022-01-03       Impact factor: 18.688

Review 3.  Elucidating the cellular dynamics of the brain with single-cell RNA sequencing.

Authors:  Aida Cardona-Alberich; Manon Tourbez; Sarah F Pearce; Christopher R Sibley
Journal:  RNA Biol       Date:  2021-01-27       Impact factor: 4.652

4.  Single cell RNA-seq analysis reveals temporally-regulated and quiescence-regulated gene expression in Drosophila larval neuroblasts.

Authors:  Noah Dillon; Ben Cocanougher; Chhavi Sood; Xin Yuan; Andrea B Kohn; Leonid L Moroz; Sarah E Siegrist; Marta Zlatic; Chris Q Doe
Journal:  Neural Dev       Date:  2022-08-24       Impact factor: 3.800

5.  Neuropeptidomic Analysis of a Genetically Defined Cell Type in Mouse Brain and Pituitary.

Authors:  Lloyd D Fricker; Alexandre K Tashima; Amanda K Fakira; Ute Hochgeschwender; William C Wetsel; Lakshmi A Devi
Journal:  Cell Chem Biol       Date:  2020-11-19       Impact factor: 8.116

  5 in total

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