Literature DB >> 26353759

Discovering New Biology through Sequencing of RNA.

Andreas P M Weber1.   

Abstract

Sequencing of RNA (RNA-Seq) was invented approximately 1 decade ago and has since revolutionized biological research. This update provides a brief historic perspective on the development of RNA-Seq and then focuses on the application of RNA-Seq in qualitative and quantitative analyses of transcriptomes. Particular emphasis is given to aspects of data analysis. Since the wet-lab and data analysis aspects of RNA-Seq are still rapidly evolving and novel applications are continuously reported, a printed review will be rapidly outdated and can only serve to provide some examples and general guidelines for planning and conducting RNA-Seq studies. Hence, selected references to frequently update online resources are given.
© 2015 American Society of Plant Biologists. All Rights Reserved.

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Year:  2015        PMID: 26353759      PMCID: PMC4634082          DOI: 10.1104/pp.15.01081

Source DB:  PubMed          Journal:  Plant Physiol        ISSN: 0032-0889            Impact factor:   8.340


  70 in total

1.  BLAT--the BLAST-like alignment tool.

Authors:  W James Kent
Journal:  Genome Res       Date:  2002-04       Impact factor: 9.043

Review 2.  Next-generation DNA sequencing methods.

Authors:  Elaine R Mardis
Journal:  Annu Rev Genomics Hum Genet       Date:  2008       Impact factor: 8.929

3.  Low-coverage massively parallel pyrosequencing of cDNAs enables proteomics in non-model species: comparison of a species-specific database generated by pyrosequencing with databases from related species for proteome analysis of pea chloroplast envelopes.

Authors:  Andrea Bräutigam; Roshan P Shrestha; Doug Whitten; Curtis G Wilkerson; Kevin M Carr; John E Froehlich; Andreas P M Weber
Journal:  J Biotechnol       Date:  2008-02-17       Impact factor: 3.307

4.  A sequencing method based on real-time pyrophosphate.

Authors:  M Ronaghi; M Uhlén; P Nyrén
Journal:  Science       Date:  1998-07-17       Impact factor: 47.728

5.  Defining a personal, allele-specific, and single-molecule long-read transcriptome.

Authors:  Hagen Tilgner; Fabian Grubert; Donald Sharon; Michael P Snyder
Journal:  Proc Natl Acad Sci U S A       Date:  2014-06-24       Impact factor: 11.205

6.  Comparative transcriptome atlases reveal altered gene expression modules between two Cleomaceae C3 and C4 plant species.

Authors:  Canan Külahoglu; Alisandra K Denton; Manuel Sommer; Janina Maß; Simon Schliesky; Thomas J Wrobel; Barbara Berckmans; Elsa Gongora-Castillo; C Robin Buell; Rüdiger Simon; Lieven De Veylder; Andrea Bräutigam; Andreas P M Weber
Journal:  Plant Cell       Date:  2014-08-08       Impact factor: 11.277

7.  A plastidial sodium-dependent pyruvate transporter.

Authors:  Tsuyoshi Furumoto; Teppei Yamaguchi; Yumiko Ohshima-Ichie; Masayoshi Nakamura; Yoshiko Tsuchida-Iwata; Masaki Shimamura; Junichi Ohnishi; Shingo Hata; Udo Gowik; Peter Westhoff; Andrea Bräutigam; Andreas P M Weber; Katsura Izui
Journal:  Nature       Date:  2011-08-24       Impact factor: 49.962

8.  Oenology: red wine procyanidins and vascular health.

Authors:  R Corder; W Mullen; N Q Khan; S C Marks; E G Wood; M J Carrier; A Crozier
Journal:  Nature       Date:  2006-11-30       Impact factor: 49.962

9.  Towards an integrative model of C4 photosynthetic subtypes: insights from comparative transcriptome analysis of NAD-ME, NADP-ME, and PEP-CK C4 species.

Authors:  Andrea Bräutigam; Simon Schliesky; Canan Külahoglu; Colin P Osborne; Andreas P M Weber
Journal:  J Exp Bot       Date:  2014-03-18       Impact factor: 6.992

10.  The role of photorespiration during the evolution of C4 photosynthesis in the genus Flaveria.

Authors:  Julia Mallmann; David Heckmann; Andrea Bräutigam; Martin J Lercher; Andreas P M Weber; Peter Westhoff; Udo Gowik
Journal:  Elife       Date:  2014-06-16       Impact factor: 8.140

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  11 in total

1.  A Revolution in Plant Metabolism: Genome-Enabled Pathway Discovery.

Authors:  Jeongwoon Kim; C Robin Buell
Journal:  Plant Physiol       Date:  2015-07-29       Impact factor: 8.340

2.  Focus Issue on Metabolism: Metabolites, Metabolites Everywhere.

Authors:  Alisdair R Fernie; Eran Pichersky
Journal:  Plant Physiol       Date:  2015-11       Impact factor: 8.340

Review 3.  How technical progress reshaped behavioral neuroendocrinology during the last 50 years… and some methodological remarks.

Authors:  Jacques Balthazart
Journal:  Horm Behav       Date:  2020-01-13       Impact factor: 3.587

4.  A Workflow Guide to RNA-seq Analysis of Chaperone Function and Beyond.

Authors:  Benjamin J Lang; Kristina M Holton; Jianlin Gong; Stuart K Calderwood
Journal:  Methods Mol Biol       Date:  2018

5.  Comparative Characterization of the Leaf Tissue of Physalis alkekengi and Physalis peruviana Using RNA-seq and Metabolite Profiling.

Authors:  Atsushi Fukushima; Michimi Nakamura; Hideyuki Suzuki; Mami Yamazaki; Eva Knoch; Tetsuya Mori; Naoyuki Umemoto; Masaki Morita; Go Hirai; Mikiko Sodeoka; Kazuki Saito
Journal:  Front Plant Sci       Date:  2016-12-20       Impact factor: 5.753

6.  Genome-Wide Identification, Localization, and Expression Analysis of Proanthocyanidin-Associated Genes in Brassica.

Authors:  Xianjun Liu; Ying Lu; Mingli Yan; Donghong Sun; Xuefang Hu; Shuyan Liu; Sheyuan Chen; Chunyun Guan; Zhongsong Liu
Journal:  Front Plant Sci       Date:  2016-12-09       Impact factor: 5.753

Review 7.  Sulphur systems biology-making sense of omics data.

Authors:  Mutsumi Watanabe; Rainer Hoefgen
Journal:  J Exp Bot       Date:  2019-08-19       Impact factor: 6.992

8.  Identification of Candidate Transcriptional Regulators of Epidermal Transfer Cell Development in Vicia faba Cotyledons.

Authors:  Kiruba S Arun-Chinnappa; David W McCurdy
Journal:  Front Plant Sci       Date:  2016-05-25       Impact factor: 5.753

9.  Post-transcriptional regulation of photosynthetic genes is a key driver of C4 leaf ontogeny.

Authors:  Nicklaus Fankhauser; Sylvain Aubry
Journal:  J Exp Bot       Date:  2016-10-18       Impact factor: 6.992

10.  OneStopRNAseq: A Web Application for Comprehensive and Efficient Analyses of RNA-Seq Data.

Authors:  Rui Li; Kai Hu; Haibo Liu; Michael R Green; Lihua Julie Zhu
Journal:  Genes (Basel)       Date:  2020-10-02       Impact factor: 4.096

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