Single-cell RNA-seq: advances and future challenges
TLDR
An overview of the biological questions single-cell RNA-seq has been used to address, the major findings obtained from such studies, and current challenges and expected future developments in this booming field are provided.Abstract:
Phenotypically identical cells can dramatically vary with respect to behavior during their lifespan and this variation is reflected in their molecular composition such as the transcriptomic landscape. Single-cell transcriptomics using next-generation transcript sequencing (RNA-seq) is now emerging as a powerful tool to profile cell-to-cell variability on a genomic scale. Its application has already greatly impacted our conceptual understanding of diverse biological processes with broad implications for both basic and clinical research. Different single-cell RNA-seq protocols have been introduced and are reviewed here—each one with its own strengths and current limitations. We further provide an overview of the biological questions single-cell RNA-seq has been used to address, the major findings obtained from such studies, and current challenges and expected future developments in this booming field.read more
Citations
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Journal ArticleDOI
Comparative Analysis of Single-Cell RNA Sequencing Methods.
Christoph Ziegenhain,Beate Vieth,Swati Parekh,Björn Reinius,Amy Guillaumet-Adkins,Martha Smets,Heinrich Leonhardt,Holger Heyn,Ines Hellmann,Wolfgang Enard +9 more
TL;DR: Power simulations at different sequencing depths showed that Drop-seq is more cost-efficient for transcriptome quantification of large numbers of cells, while MARS-seq, SCRB- sequencing, and Smart-seq2 are more efficient when analyzing fewer cells.
Journal ArticleDOI
Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing.
Darren A. Cusanovich,Riza M. Daza,Andrew Adey,Hannah A. Pliner,Lena Christiansen,Kevin L. Gunderson,Frank J. Steemers,Cole Trapnell,Jay Shendure +8 more
TL;DR: Combinatorial cellular indexing, a strategy for multiplex barcoding of thousands of single cells per experiment, was successfully used to investigate the genome-wide chromatin accessibility landscape in each of over 15,000 single cells, avoiding the need for compartmentalization of individual cells.
Journal ArticleDOI
Single-cell RNA sequencing to explore immune cell heterogeneity.
Efthymia Papalexi,Rahul Satija +1 more
TL;DR: How scRNA-seq can be used to deconvolve immune system heterogeneity by identifying novel distinct immune cell subsets in health and disease, characterizing stochastic heterogeneity within a cell population and building developmental 'trajectories' for immune cells is discussed.
Journal ArticleDOI
Comprehensive functional genomic resource and integrative model for the human brain
Daifeng Wang,Daifeng Wang,Shuang Liu,Jonathan Warrell,Hyejung Won,Xu Shi,Fabio C. P. Navarro,Declan Clarke,Mengting Gu,Prashant Emani,Yucheng T. Yang,Min Xu,Michael J. Gandal,Shaoke Lou,Jing Zhang,Jonathan J. Park,Chengfei Yan,Suhn K. Rhie,Kasidet Manakongtreecheep,Holly Zhou,Aparna Nathan,Mette A. Peters,Eugenio Mattei,Dominic Fitzgerald,Tonya M. Brunetti,Jill Moore,Yan Jiang,Kiran Girdhar,Gabriel E. Hoffman,Selim Kalayci,Zeynep H. Gümüş,Gregory E. Crawford,Panos Roussos,Schahram Akbarian,Andrew E. Jaffe,Kevin P. White,Zhiping Weng,Nenad Sestan,Daniel H. Geschwind,James A. Knowles,Mark Gerstein +40 more
TL;DR: The resource and integrative analyses have uncovered genomic elements and networks in the brain, which in turn have provided insight into the molecular mechanisms underlying psychiatric disorders.
Journal ArticleDOI
Defining cell types and states with single-cell genomics.
TL;DR: These measurements may finally make explicit the metaphor that C.H. Waddington posed nearly 60 years ago to explain cellular plasticity: Cells are residents of a vast "landscape" of possible states, over which they travel during development and in disease.
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