mRNA-Seq whole-transcriptome analysis of a single cell - PubMed (original) (raw)

doi: 10.1038/nmeth.1315. Epub 2009 Apr 6.

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

Affiliations

• PMID: 19349980
• DOI: 10.1038/nmeth.1315

mRNA-Seq whole-transcriptome analysis of a single cell

Fuchou Tang et al. Nat Methods. 2009 May.

Abstract

Next-generation sequencing technology is a powerful tool for transcriptome analysis. However, under certain conditions, only a small amount of material is available, which requires more sensitive techniques that can preferably be used at the single-cell level. Here we describe a single-cell digital gene expression profiling assay. Using our mRNA-Seq assay with only a single mouse blastomere, we detected the expression of 75% (5,270) more genes than microarray techniques and identified 1,753 previously unknown splice junctions called by at least 5 reads. Moreover, 8-19% of the genes with multiple known transcript isoforms expressed at least two isoforms in the same blastomere or oocyte, which unambiguously demonstrated the complexity of the transcript variants at whole-genome scale in individual cells. Finally, for Dicer1(-/-) and Ago2(-/-) (Eif2c2(-/-)) oocytes, we found that 1,696 and 1,553 genes, respectively, were abnormally upregulated compared to wild-type controls, with 619 genes in common.

PubMed Disclaimer

Similar articles

• mRNA-sequencing whole transcriptome analysis of a single cell on the SOLiD system.
  Lao KQ, Tang F, Barbacioru C, Wang Y, Nordman E, Lee C, Xu N, Wang X, Tuch B, Bodeau J, Siddiqui A, Surani MA. Lao KQ, et al. J Biomol Tech. 2009 Dec;20(5):266-71. J Biomol Tech. 2009. PMID: 19949700 Free PMC article.
• Genome-wide identification of targets and function of individual MicroRNAs in mouse embryonic stem cells.
  Hanina SA, Mifsud W, Down TA, Hayashi K, O'Carroll D, Lao K, Miska EA, Surani MA. Hanina SA, et al. PLoS Genet. 2010 Oct 21;6(10):e1001163. doi: 10.1371/journal.pgen.1001163. PLoS Genet. 2010. PMID: 20975942 Free PMC article.
• RNA-Seq analysis to capture the transcriptome landscape of a single cell.
  Tang F, Barbacioru C, Nordman E, Li B, Xu N, Bashkirov VI, Lao K, Surani MA. Tang F, et al. Nat Protoc. 2010 Mar;5(3):516-35. doi: 10.1038/nprot.2009.236. Epub 2010 Feb 25. Nat Protoc. 2010. PMID: 20203668 Free PMC article.
• Ago2 and GW182 expression in mouse preimplantation embryos: a link between microRNA biogenesis and GW182 protein synthesis.
  Shen XH, Han YJ, Cui XS, Kim NH. Shen XH, et al. Reprod Fertil Dev. 2010;22(4):634-43. doi: 10.1071/RD09188. Reprod Fertil Dev. 2010. PMID: 20353723
• [Transcriptomes for serial analysis of gene expression].
  Marti J, Piquemal D, Manchon L, Commes T. Marti J, et al. J Soc Biol. 2002;196(4):303-7. J Soc Biol. 2002. PMID: 12645300 Review. French.

Cited by

• The role of single-cell analyses in understanding cell lineage commitment.
  Gibson TM, Gersbach CA. Gibson TM, et al. Biotechnol J. 2013 Apr;8(4):397-407. doi: 10.1002/biot.201200201. Epub 2013 Mar 21. Biotechnol J. 2013. PMID: 23520130 Free PMC article. Review.
• Annotation of the Protein Coding Regions of the Equine Genome.
  Hestand MS, Kalbfleisch TS, Coleman SJ, Zeng Z, Liu J, Orlando L, MacLeod JN. Hestand MS, et al. PLoS One. 2015 Jun 24;10(6):e0124375. doi: 10.1371/journal.pone.0124375. eCollection 2015. PLoS One. 2015. PMID: 26107351 Free PMC article.
• Low-cost, low-input RNA-seq protocols perform nearly as well as high-input protocols.
  Combs PA, Eisen MB. Combs PA, et al. PeerJ. 2015 Mar 26;3:e869. doi: 10.7717/peerj.869. eCollection 2015. PeerJ. 2015. PMID: 25834775 Free PMC article.
• Evaluation of commercially available RNA amplification kits for RNA sequencing using very low input amounts of total RNA.
  Shanker S, Paulson A, Edenberg HJ, Peak A, Perera A, Alekseyev YO, Beckloff N, Bivens NJ, Donnelly R, Gillaspy AF, Grove D, Gu W, Jafari N, Kerley-Hamilton JS, Lyons RH, Tepper C, Nicolet CM. Shanker S, et al. J Biomol Tech. 2015 Apr;26(1):4-18. doi: 10.7171/jbt.15-2601-001. J Biomol Tech. 2015. PMID: 25649271 Free PMC article.
• In situ sequencing for RNA analysis in preserved tissue and cells.
  Ke R, Mignardi M, Pacureanu A, Svedlund J, Botling J, Wählby C, Nilsson M. Ke R, et al. Nat Methods. 2013 Sep;10(9):857-60. doi: 10.1038/nmeth.2563. Epub 2013 Jul 14. Nat Methods. 2013. PMID: 23852452

References

1. 1. Nat Genet. 2008 Dec;40(12):1413-5 - PubMed
2. 1. Genes Dev. 2007 Mar 15;21(6):644-8 - PubMed
3. 1. Genes Dev. 2007 Mar 15;21(6):682-93 - PubMed
4. 1. Dev Cell. 2004 Jan;6(1):117-31 - PubMed
5. 1. Nature. 2002 Jul 18;418(6895):293-300 - PubMed

Publication types

MeSH terms

Substances

LinkOut - more resources

• Full Text Sources

  • Nature Publishing Group

• Other Literature Sources

  • H1 Connect
  • The Lens - Patent Citations Database

• Molecular Biology Databases

  • Mouse Genome Informatics (MGI)