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RIKEN Hakubi Research Teams Microfluidics RIKEN Hakubi Research Team

RIKEN Hakubi Team Leader: Hirofumi Shintaku (D.Eng.)

Research Summary

Hirofumi  Shintaku(D.Eng.)

We actively study problems involving fluid dynamics and transport phenomena in micro/nano confined spaces. The problems are inspired by microfluidic systems for biochemical analysis and cellular engineering. Especially, we are interested in electrokinetic phenomena, e.g., electrophoresis, electroosmotic flow, and electrowetting, of complex fluids including cells and biomacromolecules. We recently developed a microfluidic system that enables the high-throughput sequencing of cytoplasmic and nuclear RNA with the physical fractionation of the RNA species via electrical lysis and isotachophoresis. We leverage our method to uncover the regulation of gene expression involving RNA localization and transport in single cells.

Main Research Fields

  • Engineering

Related Research Fields

  • Interdisciplinary Science & Engineering
  • Fluid Engineering
  • Nanobioscience
  • Nano/Microsystems


  • Microfluidics
  • Single cell analyses
  • Electrokinetics
  • Nucleic acids
  • Next generation sequencing

Selected Publications

Papers with an asterisk(*) are based on research conducted outside of RIKEN.

    • 1. Abdelmoez M.N., Oguchi, Y.,Ozaki, Y., Yokokawa, R., Kotera, H., and Shintaku, H.:
      "Distinct Kinetics in Electrophoretic Extraction of Cytoplasmic RNA from Single Cells"
      Analytical Chemistry, Vol. 92, No. 1(2020), pp. 1485-1492.
    • 2. Abdelmoez, M.N.*, Iida, K.*, Oguchi, Y.*, Nishikii, H., Yokokawa, R., Kotera, H., Uemura, S., Santiago, J.G. and Shintaku, H.:
      "SINC-seq: correlation of transient gene expressions between nucleus and cytoplasm reflects single-cell physiology"
      Genome Biology, (2018) DOI:. 10.1186/s13059-018-1446-9.
    • 3. Subramanian Parimalam, S., Oguchi, Y., Abdelmoez, M.N., Tsuchida, A., Ozaki, Y., Yokokawa, R., Kotera, H., and Shintaku, H.:
      "Electrical Lysis and RNA Extraction from Single Cells Fixed by Dithio-bis(succinimidyl propionate)"
      Analytical Chemistry, Vol. 90, No. 21 (2018), pp.12512-12518.
    • 4. *Khnouf, R., Shore, S., Han, C.M., Henderson, J.M., Munro, S.A., McCaffrey, A.P., Shintaku, H., and Santiago, J.G.:
      "Efficient Production of On-target Reads for Small RNA Sequencing of Single Cells Using Modified Adapters"
      Analytical Chemistry, Vol. 90, No. 21 (2018), pp.12609-12615.
    • 5. *Kuriyama, K.*, Shintaku, H.*, and Santiago, J.G.:
      "Protocol for microfluidic system to automate the preparation and fractionation of the nucleic acids in the cytoplasm versus nuclei of single cells"
      Bio-protocol, Vol. 6, Issue 12, (2016), e1844.
    • 6. *Kuriyama, K.*, Shintaku, H.*, and Santiago, J.G.:
      "Isotachophoresis for Fractionation and Recovery of Cytoplasmic RNA and Nucleus from Single Cells"
      Electrophoresis, Vol. 36, Issue 14(2015) pp. 1658-1662.
    • 7. *Shintaku, H., Palko, J.W., Sanders, G.M., and Santiago, J.G.:
      "Increasing Hybridization Rate and Sensitivity of Bead Based Assays Using Isotachophoresis"
      Angewandte Chemie International Edition,Vol. 53 (2014), pp. 13813-13816.
    • 8. *Shintaku, H., Nishikii, H., Marshall, L.A., Kotera, H., and Santiago, J.G.:
      "On-Chip Separation and Analysis of RNA and DNA from Single Cells"
      Analytical Chemistry, Vol. 86, No. 4 (2014), pp 1953-1957.
    • 9. *Shintaku, H., Hakamada, K., Fujimoto, H., Nagata, T., Miyake, J., and Kawano, S.:
      "Measurement of Local Electric Field in Microdevices for Low-Voltage Electroporation of Adherent Cells"
      Microsystem Technologies, Vol. 20, Issue 2 (2014), pp. 303-313.
    • 10. *Inaoka*, T., Shintaku*, H., Nakagawa, T., Kawano, S., Ogita, H., Sakamoto, T., Hamanishi, S., Wada, H., and Ito, J.:
      "Piezoelectric Materials Mimic the Function of the Cochlear Sensory Epithelium"
      Proceedings of the National Academy of Sciences of the United States of America, Vol. 108, No. 45 (2011), pp. 18390-18395.

    Annual research report

    Related Links

    Lab Members

    Principal investigator

    Hirofumi Shintaku
    RIKEN Hakubi Team Leader

    Core members

    Yusuke Oguchi
    Research Scientist
    Mahmoud Nady Abdelmoez Atta
    Postdoctoral Researcher
    Taikopaul Kaneko
    Postdoctoral Researcher
    Akifumi Shiomi
    Postdoctoral Researcher
    Koutarou Torii
    Postdoctoral Researcher
    Arata Tsuchida
    Junior Research Associate
    Kaori Nishikawa
    Technical Staff I
    Sangamithirai Subramanian parimalam
    Technical Staff II
    Masaki Nishikawa
    Visiting Scientist
    Megumi Morita

    Contact Information

    Main Research Building 6F
    2-1 Hirosawa, Wako, Saitama 351-0198, Japan
    Email: hirofumi.shintaku [at] riken.jp