Opportunities and tradeoffs in single-cell transcriptomic technologies

被引：15

作者：

Conte, Matilde I. ^{[1
]}

Fuentes-Trillo, Azahara ^{[1
]}

Conde, Cecilia Dominguez ^{[1
]}

机构：

[1] Human Technopole, Viale Rita,Levi-Montalcini 1, I-20157 Milan, Italy

来源：

TRENDS IN GENETICS | 2024年 / 40卷 / 01期

关键词：

RNA-SEQ; EXPRESSION; DYNAMICS;

D O I：

10.1016/j.tig.2023.10.003

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

Recent technological and algorithmic advances enable single-cell transcriptomic analysis with remarkable depth and breadth. Nonetheless, a persistent challenge is the compromise between the ability to profile high numbers of cells and the achievement of full-length transcript coverage. Currently, the field is progressing and developing new and creative solutions that improve cellular throughput, gene detection sensitivity and full-length transcript capture. Furthermore, longread sequencing approaches for single-cell transcripts are breaking frontiers that have previously blocked full transcriptome characterization. We here present a comprehensive overview of available options for single-cell transcriptome profiling, highlighting the key advantages and disadvantages of each approach.

引用

页码：83 / 93

页数：11

共 90 条

[1] High-throughput RNA isoform sequencing using programmed cDNA concatenation [J].

Al'Khafaji, Aziz M. ;

Smith, Jonathan T. ;

Garimella, Kiran V. ;

Babadi, Mehrtash ;

Popic, Victoria ;

Sade-Feldman, Moshe ;

Gatzen, Michael ;

Sarkizova, Siranush ;

Schwartz, Marc A. ;

Blaum, Emily M. ;

Day, Allyson ;

Costello, Maura ;

Bowers, Tera ;

Gabriel, Stacey ;

Banks, Eric ;

Philippakis, Anthony A. ;

Boland, Genevieve M. ;

Blainey, Paul C. ;

Hacohen, Nir .

NATURE BIOTECHNOLOGY, 2024, 42 (04) :582-586

[2] Single cell sequencing identifies clonally expanded synovial CD4+ TPH cells expressing GPR56 in rheumatoid arthritis [J].

Argyriou, Alexandra ;

Wadsworth, Marc H. ;

Lendvai, Adrian ;

Christensen, Stephen M. ;

Hensvold, Aase H. ;

Gerstner, Christina ;

van Vollenhoven, Annika ;

Kravarik, Kellie ;

Winkler, Aaron ;

Malmstrom, Vivianne ;

Chemin, Karine .

NATURE COMMUNICATIONS, 2022, 13 (01)

[3] Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment [J].

Azizi, Elham ;

Carr, Ambrose J. ;

Plitas, George ;

Cornish, Andrew E. ;

Konopacki, Catherine ;

Prabhakaran, Sandhya ;

Nainys, Juozas ;

Wu, Kenmin ;

Kiseliovas, Vaidotas ;

Setty, Manu ;

Choi, Kristy ;

Fromme, Rachel M. ;

Phuong Dao ;

McKenney, Peter T. ;

Wasti, Ruby C. ;

Kadaveru, Krishna ;

Mazutis, Linas ;

Rudensky, Alexander Y. ;

Pe'er, Dana .

CELL, 2018, 174 (05) :1293-+

[4] The technological landscape and applications of single-cell multi-omics [J].

Baysoy, Alev ;

Bai, Zhiliang ;

Satija, Rahul ;

Fan, Rong .

NATURE REVIEWS MOLECULAR CELL BIOLOGY, 2023, 24 (10) :695-713

[5] A human cell atlas of fetal gene expression [J].

Cao, Junyue ;

O'Day, Diana R. ;

Pliner, Hannah A. ;

Kingsley, Paul D. ;

Deng, Mei ;

Daza, Riza M. ;

Zager, Michael A. ;

Aldinger, Kimberly A. ;

Blecher-Gonen, Ronnie ;

Zhang, Fan ;

Spielmann, Malte ;

Palis, James ;

Doherty, Dan ;

Steemers, Frank J. ;

Glass, Ian A. ;

Trapnell, Cole ;

Shendure, Jay .

SCIENCE, 2020, 370 (6518) :808-+

[6] The single-cell transcriptional landscape of mammalian organogenesis [J].

Cao, Junyue ;

Spielmann, Malte ;

Qiu, Xiaojie ;

Huang, Xingfan ;

Ibrahim, Daniel M. ;

Hill, Andrew J. ;

Zhang, Fan ;

Mundlos, Stefan ;

Christiansen, Lena ;

Steemers, Frank J. ;

Trapnell, Cole ;

Shendure, Jay .

NATURE, 2019, 566 (7745) :496-+

[7] Single-Cell RNA-Seq Reveals Cellular Heterogeneity of Pluripotency Transition and X Chromosome Dynamics during Early Mouse Development [J].

Cheng, Shangli ;

Pei, Yu ;

He, Liqun ;

Peng, Guangdun ;

Reinius, Bjorn ;

Tam, Patrick P. L. ;

Jing, Naihe ;

Deng, Qiaolin .

CELL REPORTS, 2019, 26 (10) :2593-+

[8] Complete characterization of the human immune cell transcriptome using accurate full-length cDNA sequencing [J].

Cole, Charles ;

Byrne, Ashley ;

Adams, Matthew ;

Volden, Roger ;

Vollmers, Christopher .

GENOME RESEARCH, 2020, 30 (04) :589-601

[9] Cross-tissue immune cell analysis reveals tissue-specific features in humans [J].

Conde, C. Dominguez ;

Xu, C. ;

Jarvis, L. B. ;

Rainbow, D. B. ;

Wells, S. B. ;

Gomes, T. ;

Howlett, S. K. ;

Suchanek, O. ;

Polanski, K. ;

King, H. W. ;

Mamanova, L. ;

Huang, N. ;

Szabo, P. A. ;

Richardson, L. ;

Bolt, L. ;

Fasouli, E. S. ;

Mahbubani, K. T. ;

Prete, M. ;

Tuck, L. ;

Richoz, N. ;

Tuong, Z. K. ;

Campos, L. ;

Mousa, H. S. ;

Needham, E. J. ;

Pritchard, S. ;

Li, T. ;

Elmentaite, R. ;

Park, J. ;

Rahmani, E. ;

Chen, D. ;

Menon, D. K. ;

Bayraktar, O. A. ;

James, L. K. ;

Meyer, K. B. ;

Yosef, N. ;

Clatworthy, M. R. ;

Sims, P. A. ;

Farber, D. L. ;

Saeb-Parsy, K. ;

Jones, J. L. ;

Teichmann, S. A. .

SCIENCE, 2022, 376 (6594) :713-+

[10] Single-cell genomics meets human genetics [J].

Cuomo, Anna S. E. ;

Nathan, Aparna ;

Raychaudhuri, Soumya ;

MacArthur, Daniel G. ;

Powell, Joseph E. .

NATURE REVIEWS GENETICS, 2023, 24 (08) :535-549

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