caa a22 4500 606175881 CHVBK 20210128100745.0 cr unu---uuuuu 210128e20150901xx s 000 0 eng 10.1007/s00018-015-1934-y doi (NATIONALLICENCE)springer-10.1007/s00018-015-1934-y Whole transcriptome analysis with sequencing: methods, challenges and potential solutions [Elektronische Daten] [Zhihua Jiang, Xiang Zhou, Rui Li, Jennifer Michal, Shuwen Zhang, Michael Dodson, Zhiwu Zhang, Richard Harland] Whole transcriptome analysis plays an essential role in deciphering genome structure and function, identifying genetic networks underlying cellular, physiological, biochemical and biological systems and establishing molecular biomarkers that respond to diseases, pathogens and environmental challenges. Here, we review transcriptome analysis methods and technologies that have been used to conduct whole transcriptome shotgun sequencing or whole transcriptome tag/target sequencing analyses. We focus on how adaptors/linkers are added to both 5′ and 3′ ends of mRNA molecules for cloning or PCR amplification before sequencing. Challenges and potential solutions are also discussed. In brief, next generation sequencing platforms have accelerated releases of the large amounts of gene expression data. It is now time for the genome research community to assemble whole transcriptomes of all species and collect signature targets for each gene/transcript, and thus use known genes/transcripts to determine known transcriptomes directly in the near future. Springer Basel, 2015 Next generation sequencing nationallicence PolyA+ RNAs nationallicence PolyA− RNAs nationallicence Circular RNAs nationallicence RNA methylation nationallicence 5′ ends and 3′ ends nationallicence Jiang Zhihua Department of Animal Sciences, Washington State University, 99164-6351, Pullman, WA, USA aut Zhou Xiang Department of Animal Sciences, Washington State University, 99164-6351, Pullman, WA, USA aut Li Rui Department of Animal Sciences, Washington State University, 99164-6351, Pullman, WA, USA aut Michal Jennifer Department of Animal Sciences, Washington State University, 99164-6351, Pullman, WA, USA aut Zhang Shuwen Department of Animal Sciences, Washington State University, 99164-6351, Pullman, WA, USA aut Dodson Michael Department of Animal Sciences, Washington State University, 99164-6351, Pullman, WA, USA aut Zhang Zhiwu Department of Crop and Soil Sciences, Washington State University, 99164-6420, Pullman, WA, USA aut Harland Richard Department of Molecular and Cell Biology, University of California Berkeley, 94720-3200, Berkeley, CA, USA aut Cellular and Molecular Life Sciences Springer Basel 72/18(2015-09-01), 3425-3439 1420-682X 72:18<3425 2015 72 18 https://doi.org/10.1007/s00018-015-1934-y text/html Onlinezugriff via DOI BK010053 XK010053 XK010000 Metadata rights reserved Springer special CC-BY-NC licence nationallicence 1 review-article jats NATIONALLICENCE NATIONALLICENCE NL-springer NATIONALLICENCE 856 40 https://doi.org/10.1007/s00018-015-1934-y text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Jiang Zhihua Department of Animal Sciences, Washington State University, 99164-6351, Pullman, WA, USA aut NATIONALLICENCE 700 1- Zhou Xiang Department of Animal Sciences, Washington State University, 99164-6351, Pullman, WA, USA aut NATIONALLICENCE 700 1- Li Rui Department of Animal Sciences, Washington State University, 99164-6351, Pullman, WA, USA aut NATIONALLICENCE 700 1- Michal Jennifer Department of Animal Sciences, Washington State University, 99164-6351, Pullman, WA, USA aut NATIONALLICENCE 700 1- Zhang Shuwen Department of Animal Sciences, Washington State University, 99164-6351, Pullman, WA, USA aut NATIONALLICENCE 700 1- Dodson Michael Department of Animal Sciences, Washington State University, 99164-6351, Pullman, WA, USA aut NATIONALLICENCE 700 1- Zhang Zhiwu Department of Crop and Soil Sciences, Washington State University, 99164-6420, Pullman, WA, USA aut NATIONALLICENCE 700 1- Harland Richard Department of Molecular and Cell Biology, University of California Berkeley, 94720-3200, Berkeley, CA, USA aut NATIONALLICENCE 773 0- Cellular and Molecular Life Sciences Springer Basel 72/18(2015-09-01), 3425-3439 1420-682X 72:18<3425 2015 72 18