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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. Oguchi, Y., Ozaki, Y., Abdelmoez, M.N. and Shintaku, H.:
    "NanoSINC-seq dissects the isoform diversity in subcellular compartments of single cells"
    Science Advances, Vol. 7, No.15 (2021), eabe0317.
  • 2. Subramanian Parimalam, S., Abdelmoez, M.N., Tsuchida, A., Sotta, N., Tanaka, M., Kuromori, T., Fujiwara, T., Hirai, M.Y., Yokokawa, E., Oguchi, Y. and Shintaku, H.:
    "Targeted permeabilization of cell wall and extraction of charged molecules from single cells in intact plant clusters using a focused electric field"
    Analyst, Vol. 146 (2021), pp. 1604-1611.
  • 3. 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.
  • 4. 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.
  • 5. 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.
  • 6. 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.
  • 7. *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.
  • 8. *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.
  • 9. *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.
  • 10. *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.

Annual research report

Related Links

Lab Members

Principal investigator

Hirofumi Shintaku
RIKEN Hakubi Team Leader

Core members

Yusuke Oguchi
Research Scientist
Akifumi Shiomi
Special Postdoctoral Researcher
Taikopaul Kaneko
Postdoctoral Researcher
Koutarou Torii
Postdoctoral Researcher
Misa Minegishi
Visiting Researcher
Kaori Nishikawa
Technical Staff I
Arata Tsuchida
Technical Staff II
Takahiro Kuchimaru
Visiting Scientist
Megumi Morita
Mayu Kawasaki
Research Part-time Worker I
Keiko Watanabe
Research Part-time Worker II

Contact Information

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