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

[11] Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression [J].

Cuomo, Anna S. E. ;

Seaton, Daniel D. ;

McCarthy, Davis J. ;

Martinez, Iker ;

Bonder, Marc Jan ;

Garcia-Bernardo, Jose ;

Amatya, Shradha ;

Madrigal, Pedro ;

Isaacson, Abigail ;

Buettner, Florian ;

Knights, Andrew ;

Natarajan, Kedar Nath ;

Vallier, Ludovic ;

Marioni, John C. ;

Chhatriwala, Mariya ;

Stegle, Oliver .

NATURE COMMUNICATIONS, 2020, 11 (01)

[12] scHLAcount: allele-specific HLA expression from single-cell gene expression data [J].

Darby, Charlotte A. ;

Stubbington, Michael J. T. ;

Marks, Patrick J. ;

Barrio, Alvaro Martinez ;

Fiddes, Ian T. .

BIOINFORMATICS, 2020, 36 (12) :3905-3906

[13] Ultra-high-throughput single-cell RNA sequencing and perturbation screening with combinatorial fluidic indexing [J].

Datlinger, Paul ;

Rendeiro, Andre F. ;

Boenke, Thorina ;

Senekowitsch, Martin ;

Krausgruber, Thomas ;

Barreca, Daniele ;

Bock, Christoph .

NATURE METHODS, 2021, 18 (06) :635-+

[14] Specific splice junction detection in single cells with SICILIAN [J].

Dehghannasiri, Roozbeh ;

Olivieri, Julia Eve ;

Damljanovic, Ana ;

Salzman, Julia .

GENOME BIOLOGY, 2021, 22 (01)

[15] Single-Cell RNA-Seq Reveals Dynamic, Random Monoallelic Gene Expression in Mammalian Cells [J].

Deng, Qiaolin ;

Ramskold, Daniel ;

Reinius, Bjorn ;

Sandberg, Rickard .

SCIENCE, 2014, 343 (6167) :193-196

[16] Immunology in the Era of Single-Cell Technologies [J].

Efremova, Mirjana ;

Vento-Tormo, Roser ;

Park, Jong-Eun ;

Teichmann, Sarah A. ;

James, Kylie R. .

ANNUAL REVIEW OF IMMUNOLOGY, VOL 38, 2020, 38 :727-757

[17] Genomic imprinting: the emergence of an epigenetic paradigm [J].

Ferguson-Smith, Anne C. .

NATURE REVIEWS GENETICS, 2011, 12 (08) :565-575

[18] Single-cell RNA sequencing reveals ex vivo signatures of SARS-CoV-2-reactive T cells through 'reverse phenotyping' [J].

Fischer, David S. ;

Ansari, Meshal ;

Wagner, Karolin, I ;

Jarosch, Sebastian ;

Huang, Yiqi ;

Mayr, Christoph H. ;

Strunz, Maximilian ;

Lang, Niklas J. ;

D'Ippolito, Elvira ;

Hammel, Monika ;

Mateyka, Laura ;

Weber, Simone ;

Wolff, Lisa S. ;

Witter, Klaus ;

Fernandez, Isis E. ;

Leuschner, Gabriela ;

Milger, Katrin ;

Frankenberger, Marion ;

Nowak, Lorenz ;

Heinig-Menhard, Katharina ;

Koch, Ina ;

Stoleriu, Mircea G. ;

Hilgendorff, Anne ;

Behr, Juergen ;

Pichlmair, Andreas ;

Schubert, Benjamin ;

Theis, Fabian J. ;

Busch, Dirk H. ;

Schiller, Herbert B. ;

Schober, Kilian .

NATURE COMMUNICATIONS, 2021, 12 (01)

[19] Counting individual DNA molecules by the stochastic attachment of diverse labels [J].

Fu, Glenn K. ;

Hu, Jing ;

Wang, Pei-Hua ;

Fodor, Stephen P. A. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2011, 108 (22) :9026-9031

[20] Single-cell RNA sequencing coupled to TCR profiling of large granular lymphocyte leukemia T cells [J].

Gao, Shouguo ;

Wu, Zhijie ;

Arnold, Bradley ;

Diamond, Carrie ;

Batchu, Sai ;

Giudice, Valentina ;

Alemu, Lemlem ;

Raffo, Diego Quinones ;

Feng, Xingmin ;

Kajigaya, Sachiko ;

Barrett, John ;

Ito, Sawa ;

Young, Neal S. .

NATURE COMMUNICATIONS, 2022, 13 (01)

← 1 2 3 4 5 6 7 8 9 →