FY2012 Annual Report
DNA Sequencing Section
Abstract
The mission of the DNA Sequencing Section (hereinafter referred to as SQC) is to promote advances in biological science by providing researchers in genomic analyses with the latest and most advanced technologies. SQC offers OIST researchers next-generation sequencing (hereinafter abbreviated as NGS) services in a wide range of NGS applications including de novo genome sequencing, re-sequencing, RNA sequencing, and ChIP sequencing. We help researchers with their planning, library preparation, library quantification and sequencing.
As of March 2013, SQC has been equipped with seven next-generation sequencing instruments shown in the table below. An Ion Proton sequencer manufactured by Life Technologies was newly installed in January 2013 and its operation has started for OIST researchers.
| Type | Manufacturer | Qty. |
| Genome Sequencer FLX+ | Roche | 3 |
| Genome Analyzer IIx | Illumina | 1 |
| HiSeq2000 | Illumina | 1 |
| MiSeq | Illumina | 1 |
| Ion Proton | Life Technologies | 1 |
SQC moved from Okinawa Health Biotechnology Research and Development Center in Uruma city to the main campus’ Center Building in Onna village at the end of June 2012.
1. Staff
Section Leader :
Takanari Ichikawa
Acting Section Leader :
Hiroki Goto (from November, 2012)
Technical Expert :
Managu Fujie (from November, 2012)
Staff :
Shinichi Yamasaki
Nana Arakaki
Azadeh Seidi (till February 2013)
Ryo Koyanagi (from January 2013)
2. Activities
2.1. Sequencing Services
●Types of services
SQC offered the following various sequencing and library preparation services.
- De novo sequencing
- Re-sequencing
- Transcriptome
- ChIP-seq
- miRNA-seq
- Library preparations (shotgun, mate-pair/paired-end, mRNA, and small RNA with/without multiplexing)
In FY2012, SQC provided our services to the following seven units: Brenner Unit, Goryanin Unit, Luscombe Unit, Mikheyev Unit, Satoh Unit, Saze Unit, and Yanagida Unit.
●Sequencer Operation
Monthly operating of each is shown below. Genome Sequencer FLX+ shows it as the number of runs, and Illumina sequencers (Genome Analyzer IIx, HiSeq2000, and Miseq) show it as the number of cycles. (Note that Genome Analyzer IIx takes 5 days to 2 weeks per sequencing and each month in the chart shows the start date of the sequencing.) Sequencer operating rate varies depending on the number of requests but the operating rate became lower in summer because our laboratory was relocated from Uruma to Onna campus.
Genome Sequencer FLX+
Genome Analyzer IIx
HiSeq2000
MiSeq
2.2. Other activities
●Application Note
SQC provided Beckman Coulter Company with the result of data quality improvement using MoFlo XDP (flow cytometer) for bead sorting in the protocol of GS FLX+. The method was introduced at the company’s website. (See. 4.2 Books and other on-time publications)
●Technical Exchange Meeting of Okinawa NGS
Continuing from 2011, we had the periodic meeting of NGS-technical exchange among the following four institutes/universities in Okinawa: Okinawa Industrial Technology Center, Okinawa Prefectural Agricultural Research Center, the University of the Ryukyus (Tropical Biosphere Research Center and Faculty of Medicine), and us (OIST SQC). In FY2012, three meetings were held at three different venues for the purpose of the introduction of their sequencing facilities to the others (See 6. Meetings and Events). It results in deepening our understanding related to NGS in technical and equipmental aspects.
3. Publications
* SQC and SQC members are underlined.
3.1. Journal (by users)
* The article was published by OIST researchers who used our sequencing service. The author expressed their gratitude to SQC in acknowledgement in the article.
Clive S. Barker and Fadel A. Samatey
Cross-Complementation Study of the Flagellar Type III Export Apparatus Membrane Protein FlhB
PLoS One, 7(8): e44030 (2012).
3.2. Book and other on-time pulication (by SQC)
Application note
DNA Sequencing Section
Improvement of GS FLX+ sequence data using MoFlo XDP for bead sorting
URL: www.bc-cytometry.com/application/appli_topics32.html
Flow cytometry applications in the website of Beckman Coulter, Inc.
3.3. Oral and Poster Presentations (by SQC)
●Oral Presentations (all are invited presentations)
Fujie, M.
Tips for sample preparation in NGS -Usage of digital PCR-
Luncheon Seminar hosted by Bio-Rad
7th Japanese Society of Genome Microbiology, Nagahama Institute of Bio-Science and Technology, Shiga Prefecture, Japan. March 10, 2013.
Fujie, M.
Semi-automated shotgun and mate-pair library preparations for de-novo sequencing in OIST
NGS Session in “For the Better Forum 2012”
75th Anniversary Event of Perkin Elmer Japan, Roppongi Academyhills 49, Tokyo, Japan. November 15-16, 2012.
Fujie, M., Uemukai, K., Suzuki, S., and Satoh, K.
The latest method of library Construction for NGS
NGS Beginner’s Tutorial
The 2nd Meeting of NGS Field, Orbit Hall in Hotel Hankyu Expo Park, Osaka, Japan. May 24-25, 2012.
Fujie, M.
OIST SQC-oriented Library Prep.
Library Prep. Session
The 2nd Meeting of NGS Field, Orbit Hall in Hotel Hankyu Expo Park, Osaka, Japan. May 24-25, 2012.
●Poster presentations
Koyanagi, R., Seidi, A., Fujie, M., and Satoh, N.
Genome Sequencing of Botryococcus and Aurantiochytrium.
Okinawa Intellectual Cluster Program Symposium, Pacific Hotel Okinawa, Dec. 19, 2012.
Arakaki, N., Yamasaki, S., Fujie, M., Goto, H., Seidi, A., Usami, T., Yokoyama, Y., and Ichikawa, T.
Next generation management of OIST SQC
The 2nd Meeting of NGS Field, Orbit Hall in Hotel Hankyu Expo Park, May 24-25, 2012.
Goto. H., Yamasaki S., Fujie, M., Usami, T., Seidi, A., Arakaki, N., Yokoyama, Y., Ichikawa, T., Kobayashi, M., Komine, H., and Moteki, T.
Large scale automated system of NGS library preparation in OIST SQC
The 2nd Meeting of NGS Field, Orbit Hall in Hotel Hankyu Expo Park, May 24-25, 2012.
Yamasaki, S., Fujie, M., Usami, T., Goto, H., Seidi, A., Arakaki, N., Ichikawa, T., Ino, R.,
Sekiguchi, T., Yamaguchi, T., and Maeda, Y.
Data improvement through the introduction of beads sorting in Roche GS FLX+
The 2nd Meeting of NGS Field, Orbit Hall in Hotel Hankyu Expo Park, May 24-25, 2012.
4. Meetings and Events
5th Technical exchange meeting of Okinawa NGS
Fujie, M., Arakaki, N.
Okinawa Industrial Technology Center, Okinawa, June 18, 2012.
6th Technical exchange meeting of Okinawa NGS
Yamasaki, S., Fujie, M., Arakaki, N.
Okinawa Industrial Technology Center, Okinawa, November 6, 2012.
7th Technical exchange meeting of Okinawa NGS
Yamasaki, S., Goto, H., Fujie, M., Arakaki, N., Koyanagi, R.
Okinawa Institute of Science and Technology, Okinawa, March 21, 2013.