Research Summary

Selected Publications

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

• 1. Shiomi, A., Kaneko, T., Nishikawa, K., Tsuchida, A., Isoshima, T., Sato, M., Toyooka, K., Doi, K., Nishikii, H., and Shintaku, H.:
  "High-throughput mechanical phenotyping and transcriptomics of single cells"
  Nature Communications 15 (2024), 3812 (13 pages).
• 2. Tsuchida, A., Kaneko, T., Nishikawa, K., Kawasaki, M., Yokokawa, R., and Shintaku, H.:
  "Opto-combinatorial indexing enables high-content transcriptomics by linking cell images and transcriptome"
  Lab on a Chip, Vol.24 (2024), pp.2287-2297.
• 3. Minegishi, M., Kuchimaru, T., Nishikawa, K., Isagawa, T., Iwano, S., Iida, K., Hara, H., Miura, S., Sato, M., Watanabe, S., Shiomi, A., Mabuchi, Y., Hamana, H., Kishi, H., Sato, T., Sawaki, D., Sato, S., Hanazono, Y., Suzuki, A., Koro, T., Kadonosono, T., Shimogori, T., Miyawaki, A., Takeda, N., Shintaku, H., Kizaka-Kondoh, S., and Nishimura, S.:
  "Secretory GFP reconstitution labeling of neighboring cells interrogates cell?cell interactions in metastatic niches"
  Nature Communications, 14 (2023), 8031 (12 pages).
• 4. 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.
• 5. 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.
• 6. 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.
• 7. 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.
• 8. 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.
• 9. 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.
• 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

Contact Information