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Literature DB >> 21451510

Development and applications of single-cell transcriptome analysis.

Fuchou Tang¹, Kaiqin Lao, M Azim Surani.

Abstract

Dissecting the relationship between genotype and phenotype is one of the central goals in developmental biology and medicine. Transcriptome analysis is a powerful strategy to connect genotype to phenotype of a cell. Here we review the history, progress, potential applications and future developments of single-cell transcriptome analysis. In combination with live cell imaging and lineage tracing, it will be possible to decipher the full gene expression network underlying physiological functions of individual cells in embryos and adults, and to study diseases.

Entities: Chemical

Mesh：

Substances：
RNA

Year: 2011 PMID： 21451510 PMCID： PMC3408593 DOI： 10.1038/nmeth.1557

Source DB: PubMed Journal: Nat Methods ISSN： 1548-7091 Impact factor: 28.547

80 in total

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Authors: Ernest S Kawasaki
Journal: Ann N Y Acad Sci Date: 2004-05 Impact factor: 5.691

2. Amplified RNA synthesized from limited quantities of heterogeneous cDNA.

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Journal: Proc Natl Acad Sci U S A Date: 1990-03 Impact factor: 11.205

3. Visualization of single RNA transcripts in situ.

Authors: A M Femino; F S Fay; K Fogarty; R H Singer
Journal: Science Date: 1998-04-24 Impact factor: 47.728

4. 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

Review 5. Functional roles for noise in genetic circuits.

Authors: Avigdor Eldar; Michael B Elowitz
Journal: Nature Date: 2010-09-09 Impact factor: 49.962

6. Amplification-free digital gene expression profiling from minute cell quantities.

Authors: Fatih Ozsolak; David T Ting; Ben S Wittner; Brian W Brannigan; Suchismita Paul; Nabeel Bardeesy; Sridhar Ramaswamy; Patrice M Milos; Daniel A Haber
Journal: Nat Methods Date: 2010-07-18 Impact factor: 28.547

7. 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

8. MicroRNA expression profiling of single whole embryonic stem cells.

Authors: Fuchou Tang; Petra Hajkova; Sheila C Barton; Kaiqin Lao; M Azim Surani
Journal: Nucleic Acids Res Date: 2006-01-24 Impact factor: 16.971

9. Non-genetic origins of cell-to-cell variability in TRAIL-induced apoptosis.

Authors: Sabrina L Spencer; Suzanne Gaudet; John G Albeck; John M Burke; Peter K Sorger
Journal: Nature Date: 2009-04-12 Impact factor: 49.962

10. Comprehensive comparative analysis of strand-specific RNA sequencing methods.

Authors: Joshua Z Levin; Moran Yassour; Xian Adiconis; Chad Nusbaum; Dawn Anne Thompson; Nir Friedman; Andreas Gnirke; Aviv Regev
Journal: Nat Methods Date: 2010-08-15 Impact factor: 28.547

130 in total

1. Using an adherent cell culture of the mouse subependymal zone to study the behavior of adult neural stem cells on a single-cell level.

Authors: Felipe Ortega; Marcos R Costa; Tatiana Simon-Ebert; Timm Schroeder; Magdalena Götz; Benedikt Berninger
Journal: Nat Protoc Date: 2011-11-03 Impact factor: 13.491

2. Tracking the progression of the human inner cell mass during embryonic stem cell derivation.

Authors: Thomas O'Leary; Björn Heindryckx; Sylvie Lierman; David van Bruggen; Jelle J Goeman; Mado Vandewoestyne; Dieter Deforce; Susana M Chuva de Sousa Lopes; Petra De Sutter
Journal: Nat Biotechnol Date: 2012-02-26 Impact factor: 54.908

3. Mapping cell fate decisions that occur during soybean defense responses.

Authors: Prachi D Matsye; Ranjit Kumar; Parsa Hosseini; Christina M Jones; Arianne Tremblay; Nadim W Alkharouf; Benjamin F Matthews; Vincent P Klink
Journal: Plant Mol Biol Date: 2011-10-11 Impact factor: 4.076

4. Direct metabolomics for plant cells by live single-cell mass spectrometry.

Authors: Takashi Fujii; Shuichi Matsuda; Mónica Lorenzo Tejedor; Tsuyoshi Esaki; Iwao Sakane; Hajime Mizuno; Naohiro Tsuyama; Tsutomu Masujima
Journal: Nat Protoc Date: 2015-08-27 Impact factor: 13.491

Review 5. Mechanisms of fate decision and lineage commitment during haematopoiesis.

Authors: Ana Cvejic
Journal: Immunol Cell Biol Date: 2015-11-03 Impact factor: 5.126

6. Computational biology: How to catch rare cell types.

Authors: Lu Wen; Fuchou Tang
Journal: Nature Date: 2015-08-19 Impact factor: 49.962

Review 7. Single-cell analysis of the transcriptome and its application in the characterization of stem cells and early embryos.

Authors: Na Liu; Lin Liu; Xinghua Pan
Journal: Cell Mol Life Sci Date: 2014-03-21 Impact factor: 9.261