On the study of microbial transcriptomes using second- and third-generation sequencing technologies.

作者: Sang Chul Choi

DOI: 10.1007/S12275-016-6233-2

关键词:

摘要: Second-generation sequencing technologies transformed the study of microbial transcriptomes. They helped reveal transcription start sites and antisense transcripts species, improving genome annotation. Quantification genome-wide gene expression levels allowed for functional studies research. Ever-evolving are reshaping approaches to studying Recently, Oxford Nanopore Technologies delivered a platform called MinION, third-generation technology, research community. We expect it be next technology that enables breakthroughs in life science fields. The transcriptomes will no exception. In this paper, we review transcriptomics using second- generation technology. also discuss prospect with thirdgeneration sequencing.

参考文章(100)
Alexander G. Williams, Sean Thomas, Stacia K. Wyman, Alisha K. Holloway, RNA-seq Data: Challenges in and Recommendations for Experimental Design and Analysis. Current protocols in human genetics. ,vol. 83, ,(2014) , 10.1002/0471142905.HG1113S83
Nicholas J Loman, Joshua Quick, Jared T Simpson, A complete bacterial genome assembled de novo using only nanopore sequencing data Nature Methods. ,vol. 12, pp. 733- 735 ,(2015) , 10.1038/NMETH.3444
Prerana Wagle, Miloš Nikolić, Peter Frommolt, QuickNGS elevates Next-Generation Sequencing data analysis to a new level of automation BMC Genomics. ,vol. 16, pp. 487- 487 ,(2015) , 10.1186/S12864-015-1695-X
Joshua Quick, Philip Ashton, Szymon Calus, Carole Chatt, Savita Gossain, Jeremy Hawker, Satheesh Nair, Keith Neal, Kathy Nye, Tansy Peters, Elizabeth De Pinna, Esther Robinson, Keith Struthers, Mark Webber, Andrew Catto, Timothy J. Dallman, Peter Hawkey, Nicholas J. Loman, Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella Genome Biology. ,vol. 16, pp. 114- 114 ,(2015) , 10.1186/S13059-015-0677-2
Vivien Marx, Nanopores: a sequencer in your backpack Nature Methods. ,vol. 12, pp. 1015- 1018 ,(2015) , 10.1038/NMETH.3625
Günter P. Wagner, Koryu Kin, Vincent J. Lynch, Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples. Theory in Biosciences. ,vol. 131, pp. 281- 285 ,(2012) , 10.1007/S12064-012-0162-3
Bhavjinder K Dhillon, Matthew R Laird, Julie A Shay, Geoffrey L Winsor, Raymond Lo, Fazmin Nizam, Sheldon K Pereira, Nicholas Waglechner, Andrew G McArthur, Morgan GI Langille, Fiona SL Brinkman, None, IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis Nucleic Acids Research. ,vol. 43, ,(2015) , 10.1093/NAR/GKV401
Marc Güell, Vera van Noort, Eva Yus, Wei-Hua Chen, Justine Leigh-Bell, Konstantinos Michalodimitrakis, Takuji Yamada, Manimozhiyan Arumugam, Tobias Doerks, Sebastian Kühner, Michaela Rode, Mikita Suyama, Sabine Schmidt, Anne-Claude Gavin, Peer Bork, Luis Serrano, Transcriptome Complexity in a Genome-Reduced Bacterium Science. ,vol. 326, pp. 1268- 1271 ,(2009) , 10.1126/SCIENCE.1176951
Karla D. Passalacqua, Anjana Varadarajan, Charlotte Weist, Brian D. Ondov, Benjamin Byrd, Timothy D. Read, Nicholas H. Bergman, Strand-Specific RNA-Seq Reveals Ordered Patterns of Sense and Antisense Transcription in Bacillus anthracis PLoS ONE. ,vol. 7, pp. e43350- ,(2012) , 10.1371/JOURNAL.PONE.0043350
Robert D Fleischmann, Mark D Adams, Owen White, Rebecca A Clayton, Ewen F Kirkness, Anthony R Kerlavage, Carol J Bult, Jean-Francois Tomb, Brian A Dougherty, Joseph M Merrick, Keith McKenney, Granger Sutton, Will FitzHugh, Chris Fields, Jeannine D Gocayne, John Scott, Robert Shirley, Li-lng Liu, Anna Glodek, Jenny M Kelley, Janice F Weidman, Cheryl A Phillips, Tracy Spriggs, Eva Hedblom, Matthew D Cotton, Teresa R Utterback, Michael C Hanna, David T Nguyen, Deborah M Saudek, Rhonda C Brandon, Leah D Fine, Janice L Fritchman, Joyce L Fuhrmann, NSM Geoghagen, Cheryl L Gnehm, Lisa A McDonald, Keith V Small, Claire M Fraser, Hamilton O Smith, J Craig Venter, Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science. ,vol. 269, pp. 496- 512 ,(1995) , 10.1126/SCIENCE.7542800