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Scientific Publications
- De Novo Genomic Analysis
- Re-sequencing
- Genotyping
- Target Sequencing
- RNA-Seq
- Small RNA-Seq
- Amplicon-Seq
- CRISPR Screening Analysis
- Microbiome Analyses
- ChIP-Seq
List of publications in which HSS NGS services were used is available as noted below.
De Novo Genomic Analysis
Draft genome sequence of Veillonella tobetsuensis ATCC BAA-2400T isolated from human tongue biofilm.
Izumi Mashima, Futoshi Nakazawa
Genome Announc. 3.4 (2015): e00808-15.
Genome sequence of the multiple-β-lactam-antibiotic-resistant bacterium Acidovorax sp. strain MR-S7.
Takamasa Miura, Hiroyuki Kusada, Yoichi Kamagata, Satoshi Hanada, Nobutada Kimura
Genome Announc. 1.4 (2013): e00412-13.
Re-sequencing
Ongoing phenotypic and genomic changes in experimental coevolution of RNA bacteriophage Qβ and Escherichia coli.
Akiko Kashiwagi, Tetsuya Yomo
PLoS genetics 7.8 (2011): e1002188.
Genetic characterization of a Marek’s disease virus strain isolated in JapanGenetic characterization of a Marek’s disease virus strain isolated in Japan.
Shiro Murata, Yuka Machida, Masayoshi Isezaki, Naoya Maekawa, Tomohiro Okagawa, Satoru Konnai, Kazuhiko Ohashi
Virology Journal. 2020; 17: 186.
Genotyping
Genome-Wide SNP and STR Discovery in the Japanese Crested Ibis and Genetic Diversity among Founders of the Japanese Population.
Yukio Taniguchi, Hirokazu Matsuda, Takahisa Yamada, Toshie Sugiyama, Kosuke Homma, Yoshinori Kaneko, Satoshi Yamagishi, Hiroaki Iwaisaki
PloS one 8.8 (2013): e72781.
Target Sequencing
Identification of human papillomavirus (HPV) 16 DNA integration and the ensuing patterns of methylation in HPV‐associated head and neck squamous cell carcinoma cell lines.
Takashi Hatano, Daisuke Sano, Hideaki Takahashi, Hiroshi Hyakusoku, Yasuhiro Isono, Shoko Shimada, Kae Sawakuma, Kentaro Takada, Ritsuko Oikawa, Yoshiyuki Watanabe, Hiroyuki Yamamoto, Fumio Itoh, Jeffrey N. Myers, Nobuhiko Oridate
International journal of cancer 140.7 (2017): 1571-1580.
DNA methylation at hepatitis B viral integrants is associated with methylation at flanking human genomic sequences.
Yoshiyuki Watanabe, Hiroyuki Yamamoto, Ritsuko Oikawa, Minoru Toyota, Masakazu Yamamoto, Norihiro Kokudo,Shinji Tanaka, Shigeki Arii, Hiroshi Yotsuyanagi, Kazuhiko Koike, Fumio Itoh
Genome research 25.3 (2015): 328-337.
RNA-Seq
Next-Generation Sequencing of Protein-Coding and Long Non-protein-Coding RNAs in Two Types of Exosomes Derived from Human Whole Saliva.
Yuko Ogawa, Masafumi Tsujimoto, Ryohei Yanoshita
Biological and Pharmaceutical Bulletin 39.9 (2016): 1496-1507.
De novo sequence analysis of cytochrome P450 1–3 genes expressed in ostrich liver with highest expression of CYP2G19.
Yusuke K. Kawai, Kensuke P. Watanabe, Akihiro Ishii, Aiko Ohnuma, Hirofumi Sawa, Yoshinori Ikenaka, Mayumi Ishizuka
Genomics and Proteomics 8.3 (2013): 201-208.
Small RNA-Seq
Small RNA Transcriptomes of Two Types of Exosomes in Human Whole Saliva Determined by Next Generation Sequencing.
Yuko Ogawa, Yoshitaka Taketomi, Makoto Murakami, Masafumi Tsujimoto, Ryohei Yanoshita
Biological and Pharmaceutical Bulletin 36.1 (2013): 66-75.
Tandemly arranged chalcone synthase A genes contribute to the spatially regulated expression of siRNA and the natural bicolor floral phenotype in Petunia hybrida.
Yasumasa Morita, Ryoko Saito, Yusuke Ban, Natsu Tanikawa, Kazuyuki Kuchitsu, Toshio Ando, Manabu Yoshikawa, Yoshiki Habu, Yoshihiro Ozeki, Masayoshi Nakayama
The Plant Journal 70.5 (2012): 739-749.
Endogenous short interfering RNAs of chalcone synthase genes associated with inhibition of seed coat pigmentation in soybean.
Tasuku Kurauchi, Takuro Matsumoto, Akito Taneda, Teruo Sano, Mineo Senda
Breeding science 59.4 (2009): 419-426.
Amplicon-Seq
Introduction of pathogenic mutations into the mouse Psen1 gene by Base Editor and Target-AID
Hiroki Sasaguri, Kenichi Nagata, Misaki Sekiguchi, Ryo Fujioka, Yukio Matsuba, Shoko Hashimoto, Kaori Sato, Deepika Kurup, Takanori Yokota, Takaomi C Saido
Nat Commun. 2018 Jul 24;9(1):2892. doi: 10.1038/s41467-018-05262-w.
Establishment of a system for screening autophagic flux regulators using a modified fluorescent reporter and CRISPR/Cas9.
Rieko Yazawa, Yuya Nishida, Shuhei Aoyama, Isei Tanida, Takeshi Miyatsuka, Luka Suzuki, Miwa Himuro, Hidenori Haruna, Noriyuki Takubo, Toshiaki Shimizu, Hirotaka Watada
Biochemical and Biophysical Research Communications 516.3 (2019): 686-692.
Effect of High-Pressure Processing on a Wide Variety of Human Noroviruses Naturally Present in Aqua-Cultured Japanese Oysters.
Saiki Imamura, Hiromi Kanezashi, Tomoko Goshima, Atsushi Suto, You Ueki, Naoko Sugawara, Hiroshi Ito, Bizhen Zou, Chizuko Kawasaki, Tsukasa Okada, Masashi Uema, Mamoru Noda, Keiko Akimoto
Foodborne pathogens and disease 15.10 (2018): 621-626.
Next-Generation Sequencing Analysis of the Diversity of Human Noroviruses in Japanese Oysters.
Saiki Imamura, Hiromi Kanezashi, Tomoko Goshima, Mika Haruna, Tsukasa Okada, Nobuya Inagaki, Masashi Uema, Mamoru Noda, Keiko Akimoto
Foodborne pathogens and disease 14.8 (2017): 465-471.
Application of Next-Generation Sequencing to Evaluate the Profile of Noroviruses in Pre- and Post-Depurated Oysters.
Saiki Imamura, Mika Haruna, Tomoko Goshima, Hiromi Kanezashi, Tsukasa Okada, Keiko Akimoto
Foodborne pathogens and disease 13.10 (2016): 559-565.
Appication of next-generation sequencing to investigation of norovirus diversity in shellfish collected from two coastal sites in Japan from 2013 to 2014.
Saiki Imamura, Mika Haruna, Tomoko Goshima, Hiromi Kanezashi, Tsukasa Okada, Keiko Akimoto
Japanese Journal of Veterinary Research 64.2 (2016): 113-122.
Identification of male sex-linked DNA sequence of the cultured Pacific bluefin tuna Thunnus orientalis.
Yasuo Agawa, Mayui Iwaki, Takafumi Komiya, Tomoki Honryo, Kouhei Tamura, Tsukasa Okada, Naoki Yagishita, Toru Kobayashi, Yoshifumi Sawada
Fisheries science 81.1 (2015): 113-121.
CRISPR Screening Analysis
Efficient Identification of the MYC Regulator with the Use of the CRISPR Library and Context-Matched Database Screenings – PubMed (nih.gov)
Yosuke Tanaka, Hidetaka Kambayashi, Akiko Yamamoto, Iichiroh Onishi, Keisuke Sugita, Miwa Matsumura, Sachiko Ishibashi, Masumi Ikeda, Kouhei Yamamoto, Masanobu Kitagawa, Morito Kurata
Int J Mol Sci. 2022 Jul 13;23(14):7723. doi: 10.3390/ijms23147723.
Microbiome Analyses
Characterization of the salivary microbiome in healthy Thai children.
Izumi Mashima, Citra F Theodorea, Boonyanit Thaweboon, Sroisiri Thaweboon, Tippanart Vichayanrat, Frank A Scannapieco, Futoshi Nakazawa
Asian Pacific Journal of Tropical Medicine 12.4 (2019): 163.
Exploring the salivary microbiome of children stratified by the oral hygiene index.
Izumi Mashima, Citra F. Theodorea, Boonyanit Thaweboon, Sroisiri Thaweboon, Frank A. Scannapieco, Futoshi Nakazawa
PloS one 12.9 (2017): e0185274.
A novel approach, based on BLSOMs (Batch Learning Self-Organizing Maps), to the microbiome analysis of ticks.
Ryo Nakao, Takashi Abe, Ard M Nijhof, Seigo Yamamoto, Frans Jongejan, Toshimichi Ikemura, Chihiro Sugimoto
The ISME journal 7.5 (2013): 1003.
ChIP-Seq
Arid1a is essential for intestinal stem cells through Sox9 regulation.
Yukiko Hiramatsu, Akihisa Fukuda, Satoshi Ogawa, Norihiro Goto, Kozo Ikuta, Motoyuki Tsuda, Yoshihide Matsumoto, Yoshito Kimura, Takuto Yoshioka, Yutaka Takada, Takahisa Maruno, Yuta Hanyu, Tatsuaki Tsuruyama, Zhong Wang, Haruhiko Akiyama, Shigeo Takaishi, Hiroyuki Miyoshi, Makoto Mark Taketo, Tsutomu Chiba, and Hiroshi Seno
PNAS 116.5 (2019): 1704-1713.