Literature DB >> 29494575

Exponential scaling of single-cell RNA-seq in the past decade.

Valentine Svensson1,2, Roser Vento-Tormo2, Sarah A Teichmann1,2.   

Abstract

Measurement of the transcriptomes of single cells has been feasible for only a few years, but it has become an extremely popular assay. While many types of analysis can be carried out and various questions can be answered by single-cell RNA-seq, a central focus is the ability to survey the diversity of cell types in a sample. Unbiased and reproducible cataloging of gene expression patterns in distinct cell types requires large numbers of cells. Technological developments and protocol improvements have fueled consistent and exponential increases in the number of cells that can be studied in single-cell RNA-seq analyses. In this Perspective, we highlight the key technological developments that have enabled this growth in the data obtained from single-cell RNA-seq experiments.

Mesh:

Year:  2018        PMID: 29494575     DOI: 10.1038/nprot.2017.149

Source DB:  PubMed          Journal:  Nat Protoc        ISSN: 1750-2799            Impact factor:   13.491


  61 in total

1.  Quantitative analysis of mRNA amplification by in vitro transcription.

Authors:  L R Baugh; A A Hill; E L Brown; C P Hunter
Journal:  Nucleic Acids Res       Date:  2001-03-01       Impact factor: 16.971

2.  CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification.

Authors:  Tamar Hashimshony; Florian Wagner; Noa Sher; Itai Yanai
Journal:  Cell Rep       Date:  2012-08-30       Impact factor: 9.423

3.  High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization.

Authors:  Jeffrey R Moffitt; Junjie Hao; Guiping Wang; Kok Hao Chen; Hazen P Babcock; Xiaowei Zhuang
Journal:  Proc Natl Acad Sci U S A       Date:  2016-09-13       Impact factor: 11.205

4.  Analysis of multiple heterogeneous mRNAs in single cells.

Authors:  H Z Sheng; P X Lin; P G Nelson
Journal:  Anal Biochem       Date:  1994-10       Impact factor: 3.365

5.  Combined transcriptome and genome analysis of single micrometastatic cells.

Authors:  Christoph A Klein; Stefan Seidl; Karina Petat-Dutter; Sonja Offner; Jochen B Geigl; Oleg Schmidt-Kittler; Nicole Wendler; Bernward Passlick; Rudolf M Huber; Günter Schlimok; Patrick A Baeuerle; Gert Riethmüller
Journal:  Nat Biotechnol       Date:  2002-04       Impact factor: 54.908

6.  Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNA-Seq analysis.

Authors:  Fuchou Tang; Catalin Barbacioru; Siqin Bao; Caroline Lee; Ellen Nordman; Xiaohui Wang; Kaiqin Lao; M Azim Surani
Journal:  Cell Stem Cell       Date:  2010-05-07       Impact factor: 24.633

7.  Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain.

Authors:  Blue B Lake; Rizi Ai; Gwendolyn E Kaeser; Neeraj S Salathia; Yun C Yung; Rui Liu; Andre Wildberg; Derek Gao; Ho-Lim Fung; Song Chen; Raakhee Vijayaraghavan; Julian Wong; Allison Chen; Xiaoyan Sheng; Fiona Kaper; Richard Shen; Mostafa Ronaghi; Jian-Bing Fan; Wei Wang; Jerold Chun; Kun Zhang
Journal:  Science       Date:  2016-06-24       Impact factor: 47.728

8.  STRT-seq-2i: dual-index 5' single cell and nucleus RNA-seq on an addressable microwell array.

Authors:  Hannah Hochgerner; Peter Lönnerberg; Rebecca Hodge; Jaromir Mikes; Abeer Heskol; Hermann Hubschle; Philip Lin; Simone Picelli; Gioele La Manno; Michael Ratz; Jude Dunne; Syed Husain; Ed Lein; Maithreyan Srinivasan; Amit Zeisel; Sten Linnarsson
Journal:  Sci Rep       Date:  2017-11-27       Impact factor: 4.379

9.  TagGD: fast and accurate software for DNA Tag generation and demultiplexing.

Authors:  Paul Igor Costea; Joakim Lundeberg; Pelin Akan
Journal:  PLoS One       Date:  2013-03-04       Impact factor: 3.240

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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  210 in total

1.  SITC cancer immunotherapy resource document: a compass in the land of biomarker discovery.

Authors:  Siwen Hu-Lieskovan; Srabani Bhaumik; Kavita Dhodapkar; Jean-Charles J B Grivel; Sumati Gupta; Brent A Hanks; Sylvia Janetzki; Thomas O Kleen; Yoshinobu Koguchi; Amanda W Lund; Cristina Maccalli; Yolanda D Mahnke; Ruslan D Novosiadly; Senthamil R Selvan; Tasha Sims; Yingdong Zhao; Holden T Maecker
Journal:  J Immunother Cancer       Date:  2020-12       Impact factor: 13.751

2.  Self-Reporting Transposons Enable Simultaneous Readout of Gene Expression and Transcription Factor Binding in Single Cells.

Authors:  Arnav Moudgil; Michael N Wilkinson; Xuhua Chen; June He; Alexander J Cammack; Michael J Vasek; Tomás Lagunas; Zongtai Qi; Matthew A Lalli; Chuner Guo; Samantha A Morris; Joseph D Dougherty; Robi D Mitra
Journal:  Cell       Date:  2020-07-24       Impact factor: 41.582

Review 3.  The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution.

Authors:  Deanne M Taylor; Bruce J Aronow; Kai Tan; Kathrin Bernt; Nathan Salomonis; Casey S Greene; Alina Frolova; Sarah E Henrickson; Andrew Wells; Liming Pei; Jyoti K Jaiswal; Jeffrey Whitsett; Kathryn E Hamilton; Sonya A MacParland; Judith Kelsen; Robert O Heuckeroth; S Steven Potter; Laura A Vella; Natalie A Terry; Louis R Ghanem; Benjamin C Kennedy; Ingo Helbig; Kathleen E Sullivan; Leslie Castelo-Soccio; Arnold Kreigstein; Florian Herse; Martijn C Nawijn; Gerard H Koppelman; Melissa Haendel; Nomi L Harris; Jo Lynne Rokita; Yuanchao Zhang; Aviv Regev; Orit Rozenblatt-Rosen; Jennifer E Rood; Timothy L Tickle; Roser Vento-Tormo; Saif Alimohamed; Monkol Lek; Jessica C Mar; Kathleen M Loomes; David M Barrett; Prech Uapinyoying; Alan H Beggs; Pankaj B Agrawal; Yi-Wen Chen; Amanda B Muir; Lana X Garmire; Scott B Snapper; Javad Nazarian; Steven H Seeholzer; Hossein Fazelinia; Larry N Singh; Robert B Faryabi; Pichai Raman; Noor Dawany; Hongbo Michael Xie; Batsal Devkota; Sharon J Diskin; Stewart A Anderson; Eric F Rappaport; William Peranteau; Kathryn A Wikenheiser-Brokamp; Sarah Teichmann; Douglas Wallace; Tao Peng; Yang-Yang Ding; Man S Kim; Yi Xing; Sek Won Kong; Carsten G Bönnemann; Kenneth D Mandl; Peter S White
Journal:  Dev Cell       Date:  2019-03-28       Impact factor: 12.270

4.  Comprehensive Integration of Single-Cell Data.

Authors:  Tim Stuart; Andrew Butler; Paul Hoffman; Christoph Hafemeister; Efthymia Papalexi; William M Mauck; Yuhan Hao; Marlon Stoeckius; Peter Smibert; Rahul Satija
Journal:  Cell       Date:  2019-06-06       Impact factor: 41.582

Review 5.  A periodic table of cell types.

Authors:  Bo Xia; Itai Yanai
Journal:  Development       Date:  2019-06-27       Impact factor: 6.868

6.  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

Review 7.  Single cell RNA-sequencing: replicability of cell types.

Authors:  Megan Crow; Jesse Gillis
Journal:  Curr Opin Neurobiol       Date:  2019-01-09       Impact factor: 6.627

8.  Cell lineage and communication network inference via optimization for single-cell transcriptomics.

Authors:  Shuxiong Wang; Matthew Karikomi; Adam L MacLean; Qing Nie
Journal:  Nucleic Acids Res       Date:  2019-06-20       Impact factor: 16.971

Review 9.  Advancing Cancer Research and Medicine with Single-Cell Genomics.

Authors:  Bora Lim; Yiyun Lin; Nicholas Navin
Journal:  Cancer Cell       Date:  2020-04-13       Impact factor: 31.743

Review 10.  Co-expression in Single-Cell Analysis: Saving Grace or Original Sin?

Authors:  Megan Crow; Jesse Gillis
Journal:  Trends Genet       Date:  2018-08-23       Impact factor: 11.639

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