日本語

National Institutes of Natural Sciences

National Institute for Basic Biology

NIBB Departments

Functional Genomics Facility

Faculty

SHIGENOBU, Shuji
Professor
SHIGENOBU, Shuji

Research Summary

The Functional Genomics Facility is a division of the NIBB Core Research Facilities organized jointly by NIBB and NIPS for the promotion of DNA and protein studies. The facility maintains a wide array of core research equipment, ranging from standard machinery (e.g. ultracentrifuges) to cutting edge tools (e.g. next generation DNA sequencers), which amount to 90 instruments in total. The facility is dedicated to fostering collaborations with researchers both at NIBB and other academic institutions worldwide through the provision of these tools as well as expertise. Our current focus is functional genomics. We also act as a bridge between experimental biology and bioinformatics through close consultation and training.
 
We recently conducted a large scale renovation of the Functional Genomics Facility building, and as part of this, the Visitors Lab and the Visitors Office were re-designed so that visiting scientists can work more effectively during their stay. In 2018, approximately 200 researchers came to use our facility and developed active collaborations, which consequently resulted in 20 co-authored papers published.

Representative Instruments

Genomics

The advent of next-generation sequencing (NGS) technologies is transforming modern biology thanks to ultra-high-throughput DNA sequencing. Utilizing HiSeq1500, NextSeq and MiSeq (Illumina), PacBio RS II and Sequel (PacificBio Sciences), and MinION and GridION (Oxford Nanopore Technologies), the Functional Genomics Facility is committed to joint research aimed at exploring new yet otherwise inaccessible fields in basic biology.
 
During 2018, we carried out 67 NGS projects in collaboration with researchers from academic institutions throughout the world. These projects cover a wide range of species (bacteria, animals, plants, and fungi) including both model and non-model organisms, and various other applications such as genomic re-sequencing, RNA-seq and ChIP-seq.
 

2018_functional_genomics_en_fig1.jpg
Figure 1. Next-generation sequencer
 

Proteomics

Three different types of mass spectrometer and two protein sequencers, as listed below, are used for proteome studies in our facility. In 2018, we analyzed approximately 1000 samples with mass spectrometers and protein sequencers.

- LC-MS (AB SCIEX TripleTOF 5600 system)
- LC-MS (Thermo Fisher SCIENTIFIC Orbtrap Elite)
- MALDI-TOF-MS (Bruker Daltonics REFLEX III)
- LC-Q-TOF MS (Waters Q-TOF Premier)
- Protein sequencer (ABI Procise 494 HT; ABI Procise 492 cLC)

 

2018_functional_genomics_en_fig2.jpg
Figure 2. Triple TOF LC/MS/MS System
 

Other analytical instruments (excerpts)

- Cell sorter (SONY SH800) - Bioimaging analyzer (Fujifilm LAS 3000 mini; GE FLA9000)
- Laser capture microdissection system (Thermo Fisher Scientific Arcturus XT)
- Real-time PCR machine (Thermo Fisher Scientific ABI 7500)
- Ultracentrifuge (Beckman XL-80XP etc.)
- Microplate reader (PerkinElmer Nivo; Hitachi SH-9000Lab)
- Single-cell analysis system (Fluidigm C1)

Website

Reports

Selected Publications

Shigenobu, S., & Wilson, A. C. C. (2011). Genomic revelations of a mutualism: the pea aphid and its obligate bacterial symbiont. Cellular and molecular life sciences : CMLS, 68(8), 1297-1309.

The International Aphid Genomics Consortium. (2010). Genome Sequence of the Pea Aphid Acyrthosiphon pisum. PLoS Biol., 8(2):e1000313.

Shigenobu, S., Kitadate, Y., Noda, C. and Kobayashi, S. (2006). Molecular characterization of the embryonic gonads by gene expression profiling in Drosophila melanogaster. Proc. Natl. Acad. Sci. U. S. A., 103, 13728-13733

Nakabachi, A., Shigenobu, S., Sakazume, N., Shiraki, T., Hayashizaki, Y., Carninci, P., Ishikawa, H., Kudo, T. and Fukatsu, T. (2005). Transcriptome analysis of the aphid bacteriocyte, the symbiotic host cell that harbors an endocellular mutualistic bacterium, Buchnera. Proc. Natl. Acad. Sci. U. S. A., 102, 5477-5482.

Shigenobu, S., Watanabe, H., Hattori, M., Sakaki, Y. and Ishikawa, H. (2000). Genomesequence of the endocellular bacterial symbiont of aphids Buchnera sp APS. Nature, 407, 81-86.

Contact

Professor SHIGENOBU, Shuji TEL: +81 564 55 7672  E-mail: shige@nibb.ac.jp

 

 

Picture

重信 秀治_写真1