mRNA-Seq whole-transcriptome analysis of a single cell

Nature Methods

Volumn 6, Issue 5, 2009, Pages 377-382

  Tang, Fuchou ^a   Barbacioru, Catalin ^b   Wang, Yangzhou ^b   Nordman, Ellen ^b   Lee, Clarence ^b   Xu, Nanlan ^b   Wang, Xiaohui ^b   Bodeau, John ^b   Tuch, Brian B ^b   Siddiqui, Asim ^b   Lao, Kaiqin ^b   Surani, M Azim ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b APPLIED BIOSYSTEMS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARGONAUTE 2 PROTEIN; DICER; MESSENGER RNA; TRANSCRIPTOME;

ANIMAL CELL; ANIMAL EXPERIMENT; ARTICLE; BLASTOMERE; C57BL 6 MOUSE; CONTROLLED STUDY; DOWN REGULATION; FEMALE; GENE AMPLIFICATION; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE IDENTIFICATION; GENE SEQUENCE; MICROARRAY ANALYSIS; MOUSE; MRNA SEQ ASSAY; NONHUMAN; OOCYTE; PRIORITY JOURNAL; PROTEIN ANALYSIS; RNA ANALYSIS; RNA SEQUENCE; RNA SPLICING; UPREGULATION;

ALGORITHMS; ANIMALS; BLASTOMERES; CYCLIN E; DATABASES, NUCLEIC ACID; DEAD-BOX RNA HELICASES; DNA, COMPLEMENTARY; ENDORIBONUCLEASES; EUKARYOTIC INITIATION FACTOR-2; FEMALE; GENE EXPRESSION PROFILING; KRUPPEL-LIKE TRANSCRIPTION FACTORS; MICE; MICE, INBRED STRAINS; MICE, KNOCKOUT; MICE, TRANSGENIC; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OOCYTES; POLYMERASE CHAIN REACTION; PROTEIN ISOFORMS; PROTEINS; RNA, MESSENGER; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; UP-REGULATION;

EID: 67349146589     PISSN: 15487091     EISSN: 15491676     Source Type: Journal    
DOI: 10.1038/nmeth.1315     Document Type: Article

References (30)

1. Mardis, E.R. The impact of next-generation sequencing technology on genetics. Trends Genet. 24, 133-141 (2008).
2. Wold, B. & Myers, R.M. Sequence census methods for functional genomics. Nat. Methods 5, 19-21 (2008).
3. Schuster, S.C. Next-generation sequencing transforms today's biology. Nat. Methods 5, 16-18 (2008).
4. Cloonan, N. & Grimmond, S.M. Transcriptome content and dynamics at single-nucleotide resolution. Genome Biol. 9, 234 (2008).
5. Wang, Z., Gerstein, M. & Snyder, M. RNA-Seq: A revolutionary tool for transcriptomics. Nat. Rev. Genet. 10, 57-63 (2009).
6. Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L. & Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5, 621-628 (2008).
7. Cloonan, N. et al. Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat. Methods 5, 613-619 (2008).
8. Sultan, M. et al. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 321, 956-960 (2008).
9. Wang, E.T. et al. Alternative isoform regulation in human tissue transcriptomes. Nature 456, 470-476 (2008).
10. Marioni, J.C., Mason, C.E., Mane, S.M., Stephens, M. & Gilad, Y. RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays. Genome Res. 18, 1509-1517 (2008).
11. Pan, Q., Shai, O., Lee, L.J., Frey, B.J. & Blencowe, B.J. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat. Genet. 40, 1413-1415 (2008).
12. Li, H. et al. Determination of tag density required for digital transcriptome analysis: Application to an androgen-sensitive prostate cancer model. Proc. Natl. Acad. Sci. USA 105, 20179-20184 (2008).
13. Saitou, M., Barton, S.C. & Surani, M.A. A molecular programme for the specification of germ cell fate in mice. Nature 418, 293-300 (2002).
14. Chambers, I. et al. Nanog safeguards pluripotency and mediates germline development. Nature 450, 1230-1234 (2007).
15. Toyooka, Y., Shimosato, D., Murakami, K., Takahashi, K. & Niwa, H. Identification and characterization of subpopulations in undifferentiated ES cell culture. Development 135, 909-918 (2008).
16. Kurimoto, K. et al. An improved single-cell cDNA amplification method for efficient high-density oligonucleotide microarray analysis. Nucleic Acids Res. 34, e42 (2006).
17. Kurimoto, K., Yabuta, Y., Ohinata, Y. & Saitou, M. Global single-cell cDNA amplification to provide a template for representative high-density oligonucleotide microarray analysis. Nat. Protoc. 2, 739-752 (2007).
18. Maekawa, M., Yamamoto, T., Kohno, M., Takeichi, M. & Nishida, E. Requirement for ERK MAP kinase in mouse preimplantation development. Development 134, 2751-2759 (2007).
19. Blake, W.J., Kærn, M., Cantor, C.R. & Collins, J.J. Noise in eukaryotic gene expression. Nature 422, 633-637 (2003).
20. Raser, J.M. & O'Shea, E.K. Noise in gene expression: Origins, consequences, and control. Science 309, 2010-2013 (2005).
21. Hamatani, T., Carter, M.G., Sharov, A.A. & Ko, M.S. Dynamics of global gene expression changes during mouse preimplantation development. Dev. Cell 6, 117-131 (2004).
22. Tang, F. et al. Maternal microRNAs are essential for mouse zygotic development. Genes Dev. 21, 644-648 (2007).
23. Murchison, E.P. et al. Critical roles for Dicer in the female germline. Genes Dev. 21, 682-693 (2007).
24. O'Carroll, D. et al. A Slicer-independent role for Argonaute 2 in hematopoiesis and the microRNA pathway. Genes Dev. 21, 1999-2004 (2007).
25. de Vries, W.N. et al. Expression of Cre recombinase in mouse oocytes: A means to study maternal effect genes. Genesis 26, 110-112 (2000).
26. Tam, O.H. et al. Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes. Nature 453, 534-538 (2008).
27. Rambhatla, L., Patel, B., Dhanasekaran, N. & Latham, K.E. Analysis of G protein alpha subunit mRNA abundance in preimplantation mouse embryos using a rapid, quantitative RT-PCR approach. Mol. Reprod. Dev. 41, 314-324 (1995).
28. Marzluff, W.F., Wagner, E.J. & Duronio, R.J. Metabolism and regulation of canonical histone mRNAs: Life without a poly(A) tail. Nat. Rev. Genet. 9, 843-854 (2008).
29. Nagy, A., Gertsenstein, M., Vintersten, K. & Behringer, R. Recovery and in vitro culture of preimplantation stage embryos. in Manipulating the Mouse Embryo 3rd edn. 194-200 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 2003).
30. Gordon, D.M., Patashnik, O. & Kuperberg, G. New constructions for covering designs. J. Comb. Designs 3, 269-284 (1995).