Literature DB >> 28392571

Scaling by shrinking: empowering single-cell 'omics' with microfluidic devices.

Sanjay M Prakadan1,2,3, Alex K Shalek1,2,3, David A Weitz4,5.   

Abstract

Recent advances in cellular profiling have demonstrated substantial heterogeneity in the behaviour of cells once deemed 'identical', challenging fundamental notions of cell 'type' and 'state'. Not surprisingly, these findings have elicited substantial interest in deeply characterizing the diversity, interrelationships and plasticity among cellular phenotypes. To explore these questions, experimental platforms are needed that can extensively and controllably profile many individual cells. Here, microfluidic structures - whether valve-, droplet- or nanowell-based - have an important role because they can facilitate easy capture and processing of single cells and their components, reducing labour and costs relative to conventional plate-based methods while also improving consistency. In this article, we review the current state-of-the-art methodologies with respect to microfluidics for mammalian single-cell 'omics' and discuss challenges and future opportunities.

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Mesh:

Year:  2017        PMID: 28392571      PMCID: PMC5495114          DOI: 10.1038/nrg.2017.15

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  152 in total

1.  Microfluidic device for single-cell analysis.

Authors:  Aaron R Wheeler; William R Throndset; Rebecca J Whelan; Andrew M Leach; Richard N Zare; Yish Hann Liao; Kevin Farrell; Ian D Manger; Antoine Daridon
Journal:  Anal Chem       Date:  2003-07-15       Impact factor: 6.986

2.  Single-cell proteomic chip for profiling intracellular signaling pathways in single tumor cells.

Authors:  Qihui Shi; Lidong Qin; Wei Wei; Feng Geng; Rong Fan; Young Shik Shin; Deliang Guo; Leroy Hood; Paul S Mischel; James R Heath
Journal:  Proc Natl Acad Sci U S A       Date:  2011-12-27       Impact factor: 11.205

3.  Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development.

Authors:  Sean C Bendall; Kara L Davis; El-Ad David Amir; Michelle D Tadmor; Erin F Simonds; Tiffany J Chen; Daniel K Shenfeld; Garry P Nolan; Dana Pe'er
Journal:  Cell       Date:  2014-04-24       Impact factor: 41.582

Review 4.  The future is now: single-cell genomics of bacteria and archaea.

Authors:  Paul C Blainey
Journal:  FEMS Microbiol Rev       Date:  2013-02-11       Impact factor: 16.408

5.  Reproducible copy number variation patterns among single circulating tumor cells of lung cancer patients.

Authors:  Xiaohui Ni; Minglei Zhuo; Zhe Su; Jianchun Duan; Yan Gao; Zhijie Wang; Chenghang Zong; Hua Bai; Alec R Chapman; Jun Zhao; Liya Xu; Tongtong An; Qi Ma; Yuyan Wang; Meina Wu; Yu Sun; Shuhang Wang; Zhenxiang Li; Xiaodan Yang; Jun Yong; Xiao-Dong Su; Youyong Lu; Fan Bai; X Sunney Xie; Jie Wang
Journal:  Proc Natl Acad Sci U S A       Date:  2013-12-09       Impact factor: 11.205

6.  Low Dimensionality in Gene Expression Data Enables the Accurate Extraction of Transcriptional Programs from Shallow Sequencing.

Authors:  Graham Heimberg; Rajat Bhatnagar; Hana El-Samad; Matt Thomson
Journal:  Cell Syst       Date:  2016-04-27       Impact factor: 10.304

Review 7.  Heterogeneity in immune responses: from populations to single cells.

Authors:  Rahul Satija; Alex K Shalek
Journal:  Trends Immunol       Date:  2014-04-16       Impact factor: 16.687

8.  A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response.

Authors:  Britt Adamson; Thomas M Norman; Marco Jost; Min Y Cho; James K Nuñez; Yuwen Chen; Jacqueline E Villalta; Luke A Gilbert; Max A Horlbeck; Marco Y Hein; Ryan A Pak; Andrew N Gray; Carol A Gross; Atray Dixit; Oren Parnas; Aviv Regev; Jonathan S Weissman
Journal:  Cell       Date:  2016-12-15       Impact factor: 41.582

9.  Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer.

Authors:  Jens G Lohr; Viktor A Adalsteinsson; Kristian Cibulskis; Atish D Choudhury; Mara Rosenberg; Peter Cruz-Gordillo; Joshua M Francis; Cheng-Zhong Zhang; Alex K Shalek; Rahul Satija; John J Trombetta; Diana Lu; Naren Tallapragada; Narmin Tahirova; Sora Kim; Brendan Blumenstiel; Carrie Sougnez; Alarice Lowe; Bang Wong; Daniel Auclair; Eliezer M Van Allen; Mari Nakabayashi; Rosina T Lis; Gwo-Shu M Lee; Tiantian Li; Matthew S Chabot; Amy Ly; Mary-Ellen Taplin; Thomas E Clancy; Massimo Loda; Aviv Regev; Matthew Meyerson; William C Hahn; Philip W Kantoff; Todd R Golub; Gad Getz; Jesse S Boehm; J Christopher Love
Journal:  Nat Biotechnol       Date:  2014-04-20       Impact factor: 54.908

10.  A microfluidic platform enabling single-cell RNA-seq of multigenerational lineages.

Authors:  Robert J Kimmerling; Gregory Lee Szeto; Jennifer W Li; Alex S Genshaft; Samuel W Kazer; Kristofor R Payer; Jacob de Riba Borrajo; Paul C Blainey; Darrell J Irvine; Alex K Shalek; Scott R Manalis
Journal:  Nat Commun       Date:  2016-01-06       Impact factor: 14.919

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  80 in total

1.  Droplet CAR-Wash: continuous picoliter-scale immunocapture and washing.

Authors:  Steven R Doonan; Melissa Lin; Ryan C Bailey
Journal:  Lab Chip       Date:  2019-04-23       Impact factor: 6.799

2.  Rapid single-molecule digital detection of protein biomarkers for continuous monitoring of systemic immune disorders.

Authors:  Yujing Song; Erin Sandford; Yuzi Tian; Qingtian Yin; Andrew G Kozminski; Shiuan-Haur Su; Tao Cai; Yuxuan Ye; Meng Ting Chung; Ryan Lindstrom; Annika Goicochea; Jenny Barabas; Mary Olesnavich; Michelle Rozwadowski; Yongqing Li; Hasan B Alam; Benjamin H Singer; Monalisa Ghosh; Sung Won Choi; Muneesh Tewari; Katsuo Kurabayashi
Journal:  Blood       Date:  2021-03-25       Impact factor: 22.113

Review 3.  The interplay of epigenetic marks during stem cell differentiation and development.

Authors:  Yaser Atlasi; Hendrik G Stunnenberg
Journal:  Nat Rev Genet       Date:  2017-08-14       Impact factor: 53.242

Review 4.  Integration of microbiology, molecular pathology, and epidemiology: a new paradigm to explore the pathogenesis of microbiome-driven neoplasms.

Authors:  Tsuyoshi Hamada; Jonathan A Nowak; Danny A Milner; Mingyang Song; Shuji Ogino
Journal:  J Pathol       Date:  2019-02-20       Impact factor: 7.996

5.  Three-dimensional Printing of Thermoplastic Materials to Create Automated Syringe Pumps with Feedback Control for Microfluidic Applications.

Authors:  Ming-Cheng Chen; John R Lake; Keith C Heyde; Warren C Ruder
Journal:  J Vis Exp       Date:  2018-08-30       Impact factor: 1.355

6.  Immersed AC electrospray (iACE) for monodispersed aqueous droplet generation.

Authors:  Zehao Pan; Yongfan Men; Satyajyoti Senapati; Hsueh-Chia Chang
Journal:  Biomicrofluidics       Date:  2018-08-16       Impact factor: 2.800

7.  3D-printed miniaturized fluidic tools in chemistry and biology.

Authors:  C K Dixit; K Kadimisetty; J Rusling
Journal:  Trends Analyt Chem       Date:  2018-07-05       Impact factor: 12.296

8.  A Chemical Approach for Profiling Intracellular AKT Signaling Dynamics from Single Cells.

Authors:  Shiqun Shao; Zhonghan Li; Hanjun Cheng; Siwen Wang; Nicole G Perkins; Priyanka Sarkar; Wei Wei; Min Xue
Journal:  J Am Chem Soc       Date:  2018-10-12       Impact factor: 15.419

9.  Combined Numerical and Experimental Investigation of Localized Electroporation-Based Cell Transfection and Sampling.

Authors:  Prithvijit Mukherjee; S Shiva P Nathamgari; John A Kessler; Horacio D Espinosa
Journal:  ACS Nano       Date:  2018-11-27       Impact factor: 15.881

Review 10.  Targeting minimal residual disease: a path to cure?

Authors:  Marlise R Luskin; Mark A Murakami; Scott R Manalis; David M Weinstock
Journal:  Nat Rev Cancer       Date:  2018-01-29       Impact factor: 60.716

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