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RNA-seq for transcriptome analysis in non-model plants

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Title RNA-seq for transcriptome analysis in non-model plants
Legume Genomics: methods and protocols
Springer Protocols
 
Creator Garg, Rohini
Jain, Mukesh
 
Subject RNA-seq
Transcriptome
Assembly
Next-generation sequencing
Quality control
Expression analysis
 
Description Accepted date: 05 August 2013
Sequencing of mRNA using next-generation sequencing (NGS) technologies (RNA-seq) has the potential to reveal unprecedented complexity of the transcriptomes. The transcriptome sequencing of an organism provides quick insights into the gene space, opportunity to isolate genes of interest, development of functional markers, quantitation of gene expression, and comparative genomic studies. Although becoming cheaper, transcriptome sequencing still remains an expensive endeavor. Further, the assembly of millions and billions of RNA-seq reads to construct the complete transcriptome poses great informatics challenges. Here, first we outline various important issues from experimental design to data analysis, including various strategies of transcriptome assembly, which need substantial consideration for a successful RNA-seq experiment. Further, we describe a method for using RNA-seq to characterize the transcriptome of a plant species, taking the example of a legume crop plant chickpea. Our aim is to provide a quick start guide to the nonexpert researchers for NGS-based transcriptome analysis.
This work was supported by the Department of Biotechnology,
Government of India, under the Next Generation Challenge
Programme on Chickpea Genomics (research grant no. BT/
PR12919/AGR/02/676/2009). R.G. acknowledges the award of INSPIRE Faculty Award from the Department of Science
& Technology, Government of India. M.J. acknowledges the award
of a fellowship under the Cutting-edge Research Enhancement and
Scientific Training scheme from the Department of Biotechnology,
Government of India.
 
Date 2015-11-03T06:56:03Z
2015-11-03T06:56:03Z
2013
 
Type Book chapter
 
Identifier Methods Mol. Biol., 1069: 43-58
978-1-62703-613-9
http://link.springer.com/protocol/10.1007%2F978-1-62703-613-9_4
http://172.16.0.77:8080/jspui/handle/123456789/307
 
Language en_US
 
Publisher Springer