Please use this identifier to cite or link to this item: http://223.31.159.10:8080/jspui/handle/123456789/307
Title: RNA-seq for transcriptome analysis in non-model plants
Other Titles: Legume Genomics: methods and protocols
Springer Protocols
Authors: Garg, Rohini
Jain, Mukesh
Keywords: RNA-seq
Transcriptome
Assembly
Next-generation sequencing
Quality control
Expression analysis
Issue Date: 2013
Publisher: Springer
Citation: Methods Mol. Biol., 1069: 43-58
Abstract: 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.
Description: Accepted date: 05 August 2013
URI: http://172.16.0.77:8080/jspui/handle/123456789/307
ISSN: 978-1-62703-613-9
Appears in Collections:Institutional Publications

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