RIKEN Hakubi Research Teams Microfluidics RIKEN Hakubi Research Team
RIKEN Hakubi Team Leader: Hirofumi Shintaku (D.Eng.)
Research Summary

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
Keywords
- 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. - Hirofumi Shintaku
- RIKEN Hakubi Team Leader
- 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
- Assistant
Annual research report
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Lab Members
Principal investigator
Core members
Contact Information
Main Research Building 6F
2-1 Hirosawa, Wako, Saitama 351-0198, Japan
Email: hirofumi.shintaku [at] riken.jp