Single-Cell Genome and Transcriptome Processing Prior to High-Throughput Sequencing

  • Ana M. Aransay
  • Laura Barcena
  • Aintzane Gonzalez-Lahera
  • Nuria Macias-Camara
Part of the Methods in Molecular Biology book series (MIMB, volume 1293)


Single-cell genome and transcriptome characterizations will probe to be decisive within the stem cells research, especially to describe appropriately the genetic impact of the diverse stem cells populations that are present in each organism. In the present chapter, we describe in detail how to prepare sequencing libraries out of single cells, for whole genome DNA and mRNA sequencing.

Key words

Single-cell genome Single-cell transcriptome Sequencing library High-throughput sequencing (HTS) 



We would like to thank Juan José Fuentes Nuño for his assistance on single-cell isolation procedure description. A.G.L. and some research expenses are partially supported by CIBERehd. A.M.A., N.M., A.G.L., L.B., and research expenses are supported by the Basque Country Government (Etortek Research Programs 2010/2014) and Bizkaia County’s Innovation Technology Department.


  1. 1.
    Metzker ML (2010) Sequencing technologies – the next generation. Nat Rev Genet 11(1):31–46PubMedCrossRefGoogle Scholar
  2. 2.
    Mardis ER (2011) A decade’s perspective on DNA sequencing technology. Nature 470(7333):198–203PubMedCrossRefGoogle Scholar
  3. 3.
    Evanko D (2014) Method of the Year 2013. Nat Methods 11(1):1–112Google Scholar
  4. 4.
    Zong C et al (2012) Genome-wide detection of single-nucleotide and copy-number variations of a single human cell. Science 338(6114):1622–1626PubMedCentralPubMedCrossRefGoogle Scholar
  5. 5.
    Emmert-Buck MR et al (1996) Laser capture microdissection. Science 274(5289):998–1001PubMedCrossRefGoogle Scholar
  6. 6.
    Nakamura N et al (2007) Laser capture microdissection for analysis of single cells. Methods Mol Med 132:11–18PubMedGoogle Scholar
  7. 7.
    Kuppers R, Schneider M, Hansmann ML (2013) Laser-based microdissection of single cells from tissue sections and PCR analysis of rearranged immunoglobulin genes from isolated normal and malignant human B cells. Methods Mol Biol 971:49–63PubMedGoogle Scholar
  8. 8.
    Fulwyler MJ (1965) Electronic separation of biological cells by volume. Science 150(3698):910–911PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media LLC New York 2015

Authors and Affiliations

  • Ana M. Aransay
    • 1
  • Laura Barcena
    • 2
  • Aintzane Gonzalez-Lahera
    • 1
  • Nuria Macias-Camara
    • 2
  1. 1.Genome Analysis PlatformCIC bioGUNE & CIBERehdDerioSpain
  2. 2.Genome Analysis PlatformCIC bioGUNEDerioSpain

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