Literature DB >> 35044670

Single-Cell RNA-Seq Technologies and Computational Analysis Tools: Application in Cancer Research.

Qianqian Song1, Liang Liu2,3.   

Abstract

The recent maturation of single-cell RNA sequencing (scRNA-seq) provides unique opportunities for researchers to uncover new and potentially unexpected biological discoveries and to understand the complexity of tissues by transcriptomic profiling in individual cells. This review introduces the latest scRNA-seq techniques and platforms as well as their advantages and disadvantages. Moreover, we review computational tools and pipelines for analyzing scRNA-seq data, and their applications in cancer research, highlighting the important role of scRNA-seq techniques in this area.
© 2022. Springer Science+Business Media, LLC, part of Springer Nature.

Entities:  

Keywords:  Biomarker; Cancer; Computational analysis; Single-cell RNA sequencing

Mesh:

Year:  2022        PMID: 35044670     DOI: 10.1007/978-1-0716-1896-7_23

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN: 1064-3745


  74 in total

1.  Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells.

Authors:  Allon M Klein; Linas Mazutis; Ilke Akartuna; Naren Tallapragada; Adrian Veres; Victor Li; Leonid Peshkin; David A Weitz; Marc W Kirschner
Journal:  Cell       Date:  2015-05-21       Impact factor: 41.582

2.  Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets.

Authors:  Evan Z Macosko; Anindita Basu; Rahul Satija; James Nemesh; Karthik Shekhar; Melissa Goldman; Itay Tirosh; Allison R Bialas; Nolan Kamitaki; Emily M Martersteck; John J Trombetta; David A Weitz; Joshua R Sanes; Alex K Shalek; Aviv Regev; Steven A McCarroll
Journal:  Cell       Date:  2015-05-21       Impact factor: 41.582

3.  Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma.

Authors:  Anoop P Patel; Itay Tirosh; John J Trombetta; Alex K Shalek; Shawn M Gillespie; Hiroaki Wakimoto; Daniel P Cahill; Brian V Nahed; William T Curry; Robert L Martuza; David N Louis; Orit Rozenblatt-Rosen; Mario L Suvà; Aviv Regev; Bradley E Bernstein
Journal:  Science       Date:  2014-06-12       Impact factor: 47.728

4.  Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq.

Authors:  Itay Tirosh; Benjamin Izar; Sanjay M Prakadan; Marc H Wadsworth; Daniel Treacy; John J Trombetta; Asaf Rotem; Christopher Rodman; Christine Lian; George Murphy; Mohammad Fallahi-Sichani; Ken Dutton-Regester; Jia-Ren Lin; Ofir Cohen; Parin Shah; Diana Lu; Alex S Genshaft; Travis K Hughes; Carly G K Ziegler; Samuel W Kazer; Aleth Gaillard; Kellie E Kolb; Alexandra-Chloé Villani; Cory M Johannessen; Aleksandr Y Andreev; Eliezer M Van Allen; Monica Bertagnolli; Peter K Sorger; Ryan J Sullivan; Keith T Flaherty; Dennie T Frederick; Judit Jané-Valbuena; Charles H Yoon; Orit Rozenblatt-Rosen; Alex K Shalek; Aviv Regev; Levi A Garraway
Journal:  Science       Date:  2016-04-08       Impact factor: 47.728

5.  Defining murine organogenesis at single-cell resolution reveals a role for the leukotriene pathway in regulating blood progenitor formation.

Authors:  Ximena Ibarra-Soria; Wajid Jawaid; Blanca Pijuan-Sala; Vasileios Ladopoulos; Antonio Scialdone; David J Jörg; Richard C V Tyser; Fernando J Calero-Nieto; Carla Mulas; Jennifer Nichols; Ludovic Vallier; Shankar Srinivas; Benjamin D Simons; Berthold Göttgens; John C Marioni
Journal:  Nat Cell Biol       Date:  2018-01-08       Impact factor: 28.824

6.  Single-cell RNA-sequencing uncovers transcriptional states and fate decisions in haematopoiesis.

Authors:  Emmanouil I Athanasiadis; Jan G Botthof; Helena Andres; Lauren Ferreira; Pietro Lio; Ana Cvejic
Journal:  Nat Commun       Date:  2017-12-11       Impact factor: 14.919

7.  Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput.

Authors:  Todd M Gierahn; Marc H Wadsworth; Travis K Hughes; Bryan D Bryson; Andrew Butler; Rahul Satija; Sarah Fortune; J Christopher Love; Alex K Shalek
Journal:  Nat Methods       Date:  2017-02-13       Impact factor: 28.547

8.  Single-Cell RNA-Sequencing Reveals a Continuous Spectrum of Differentiation in Hematopoietic Cells.

Authors:  Iain C Macaulay; Valentine Svensson; Charlotte Labalette; Lauren Ferreira; Fiona Hamey; Thierry Voet; Sarah A Teichmann; Ana Cvejic
Journal:  Cell Rep       Date:  2016-01-21       Impact factor: 9.423

9.  The Human Cell Atlas.

Authors:  Aviv Regev; Sarah A Teichmann; Eric S Lander; Ido Amit; Christophe Benoist; Ewan Birney; Bernd Bodenmiller; Peter Campbell; Piero Carninci; Menna Clatworthy; Hans Clevers; Bart Deplancke; Ian Dunham; James Eberwine; Roland Eils; Wolfgang Enard; Andrew Farmer; Lars Fugger; Berthold Göttgens; Nir Hacohen; Muzlifah Haniffa; Martin Hemberg; Seung Kim; Paul Klenerman; Arnold Kriegstein; Ed Lein; Sten Linnarsson; Emma Lundberg; Joakim Lundeberg; Partha Majumder; John C Marioni; Miriam Merad; Musa Mhlanga; Martijn Nawijn; Mihai Netea; Garry Nolan; Dana Pe'er; Anthony Phillipakis; Chris P Ponting; Stephen Quake; Wolf Reik; Orit Rozenblatt-Rosen; Joshua Sanes; Rahul Satija; Ton N Schumacher; Alex Shalek; Ehud Shapiro; Padmanee Sharma; Jay W Shin; Oliver Stegle; Michael Stratton; Michael J T Stubbington; Fabian J Theis; Matthias Uhlen; Alexander van Oudenaarden; Allon Wagner; Fiona Watt; Jonathan Weissman; Barbara Wold; Ramnik Xavier; Nir Yosef
Journal:  Elife       Date:  2017-12-05       Impact factor: 8.140

10.  Single-cell transcriptomics reconstructs fate conversion from fibroblast to cardiomyocyte.

Authors:  Ziqing Liu; Li Wang; Joshua D Welch; Hong Ma; Yang Zhou; Haley Ruth Vaseghi; Shuo Yu; Joseph Blake Wall; Sahar Alimohamadi; Michael Zheng; Chaoying Yin; Weining Shen; Jan F Prins; Jiandong Liu; Li Qian
Journal:  Nature       Date:  2017-10-25       Impact factor: 49.962

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