Literature DB >> 27442339

Single-cell RNA-sequencing: The future of genome biology is now.

Simone Picelli1.   

Abstract

Genome-wide single-cell analysis represents the ultimate frontier of genomics research. In particular, single-cell RNA-sequencing (scRNA-seq) studies have been boosted in the last few years by an explosion of new technologies enabling the study of the transcriptomic landscape of thousands of single cells in complex multicellular organisms. More sensitive and automated methods are being continuously developed and promise to deliver better data quality and higher throughput with less hands-on time. The outstanding amount of knowledge that is going to be gained from present and future studies will have a profound impact in many aspects of our society, from the introduction of truly tailored cancer treatments, to a better understanding of antibiotic resistance and host-pathogen interactions; from the discovery of the mechanisms regulating stem cell differentiation to the characterization of the early event of human embryogenesis.

Entities:  

Keywords:  CEL-seq; CytoSeq; Drop-seq; MARS-seq; Nanopore; RNA-sequencing; SMART-seq2; STRT/C1; Tn5 transposase; single-cell

Mesh:

Substances:

Year:  2016        PMID: 27442339      PMCID: PMC5449089          DOI: 10.1080/15476286.2016.1201618

Source DB:  PubMed          Journal:  RNA Biol        ISSN: 1547-6286            Impact factor:   4.652


  62 in total

Review 1.  LNA: a versatile tool for therapeutics and genomics.

Authors:  Michael Petersen; Jesper Wengel
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2.  Counting absolute numbers of molecules using unique molecular identifiers.

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Journal:  Nat Methods       Date:  2011-11-20       Impact factor: 28.547

Review 3.  Design and Analysis of Single-Cell Sequencing Experiments.

Authors:  Dominic Grün; Alexander van Oudenaarden
Journal:  Cell       Date:  2015-11-05       Impact factor: 41.582

4.  Thermostabilization and thermoactivation of thermolabile enzymes by trehalose and its application for the synthesis of full length cDNA.

Authors:  P Carninci; Y Nishiyama; A Westover; M Itoh; S Nagaoka; N Sasaki; Y Okazaki; M Muramatsu; Y Hayashizaki
Journal:  Proc Natl Acad Sci U S A       Date:  1998-01-20       Impact factor: 11.205

5.  Full-length cDNA cloning and determination of mRNA 5' and 3' ends by amplification of adaptor-ligated cDNA.

Authors:  A Chenchik; L Diachenko; F Moqadam; V Tarabykin; S Lukyanov; P D Siebert
Journal:  Biotechniques       Date:  1996-09       Impact factor: 1.993

6.  Low-Cost, High-Throughput Sequencing of DNA Assemblies Using a Highly Multiplexed Nextera Process.

Authors:  Elaine B Shapland; Victor Holmes; Christopher D Reeves; Elena Sorokin; Maxime Durot; Darren Platt; Christopher Allen; Jed Dean; Zach Serber; Jack Newman; Sunil Chandran
Journal:  ACS Synth Biol       Date:  2015-05-06       Impact factor: 5.110

Review 7.  Computational and analytical challenges in single-cell transcriptomics.

Authors:  Oliver Stegle; Sarah A Teichmann; John C Marioni
Journal:  Nat Rev Genet       Date:  2015-01-28       Impact factor: 53.242

8.  Entering the era of single-cell transcriptomics in biology and medicine.

Authors:  Rickard Sandberg
Journal:  Nat Methods       Date:  2014-01       Impact factor: 28.547

9.  Single-cell triple omics sequencing reveals genetic, epigenetic, and transcriptomic heterogeneity in hepatocellular carcinomas.

Authors:  Yu Hou; Huahu Guo; Chen Cao; Xianlong Li; Boqiang Hu; Ping Zhu; Xinglong Wu; Lu Wen; Fuchou Tang; Yanyi Huang; Jirun Peng
Journal:  Cell Res       Date:  2016-02-23       Impact factor: 25.617

10.  An improved single-cell cDNA amplification method for efficient high-density oligonucleotide microarray analysis.

Authors:  Kazuki Kurimoto; Yukihiro Yabuta; Yasuhide Ohinata; Yukiko Ono; Kenichiro D Uno; Rikuhiro G Yamada; Hiroki R Ueda; Mitinori Saitou
Journal:  Nucleic Acids Res       Date:  2006-03-17       Impact factor: 16.971

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  65 in total

1.  Single-cell transcriptomics from human pancreatic islets: sample preparation matters.

Authors:  Lori L Bonnycastle; Derek E Gildea; Tingfen Yan; Narisu Narisu; Amy J Swift; Tyra G Wolfsberg; Michael R Erdos; Francis S Collins
Journal:  Biol Methods Protoc       Date:  2020-01-16

2.  Single-Cell Sequencing and Organoids: A Powerful Combination for Modelling Organ Development and Diseases.

Authors:  Yuebang Yin; Peng-Yu Liu; Yinghua Shi; Ping Li
Journal:  Rev Physiol Biochem Pharmacol       Date:  2021       Impact factor: 5.545

3.  RNA in Disease and development.

Authors:  Andrea Barta; Michael F Jantsch
Journal:  RNA Biol       Date:  2017-05-04       Impact factor: 4.652

Review 4.  Power in Numbers: Single-Cell RNA-Seq Strategies to Dissect Complex Tissues.

Authors:  Kenneth D Birnbaum
Journal:  Annu Rev Genet       Date:  2018-09-07       Impact factor: 16.830

5.  Canonical Wnt signaling regulates patterning, differentiation and nucleogenesis in mouse hypothalamus and prethalamus.

Authors:  Elizabeth A Newman; Dan Wu; Makoto Mark Taketo; Jiangyang Zhang; Seth Blackshaw
Journal:  Dev Biol       Date:  2018-07-29       Impact factor: 3.582

6.  Using single-cell transcriptomics to understand functional states and interactions in microbial eukaryotes.

Authors:  Chuan Ku; Arnau Sebé-Pedrós
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2019-10-07       Impact factor: 6.237

7.  A diffusion-based microfluidic device for single-cell RNA-seq.

Authors:  Mimosa Sarma; Jiyoung Lee; Sai Ma; Song Li; Chang Lu
Journal:  Lab Chip       Date:  2019-03-27       Impact factor: 6.799

Review 8.  Islet-immune interactions in type 1 diabetes: the nexus of beta cell destruction.

Authors:  L Peters; A Posgai; T M Brusko
Journal:  Clin Exp Immunol       Date:  2019-08-14       Impact factor: 4.330

9.  Simultaneous quantification of mRNA and protein in single cells reveals post-transcriptional effects of genetic variation.

Authors:  Christian Brion; Sheila M Lutz; Frank Wolfgang Albert
Journal:  Elife       Date:  2020-11-16       Impact factor: 8.140

Review 10.  Going the Distance: Optimizing RNA-Seq Strategies for Transcriptomic Analysis of Complex Viral Genomes.

Authors:  Daniel P Depledge; Ian Mohr; Angus C Wilson
Journal:  J Virol       Date:  2018-12-10       Impact factor: 5.103

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