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DC Field | Value | Language |
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dc.contributor.author | Garg, Rohini | - |
dc.contributor.author | Jain, Mukesh | - |
dc.date.accessioned | 2015-11-03T06:56:03Z | - |
dc.date.available | 2015-11-03T06:56:03Z | - |
dc.date.issued | 2013 | - |
dc.identifier.citation | Methods Mol. Biol., 1069: 43-58 | en_US |
dc.identifier.issn | 978-1-62703-613-9 | - |
dc.identifier.other | http://link.springer.com/protocol/10.1007%2F978-1-62703-613-9_4 | - |
dc.identifier.uri | http://172.16.0.77:8080/jspui/handle/123456789/307 | - |
dc.description | Accepted date: 05 August 2013 | en_US |
dc.description.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. | en_US |
dc.description.sponsorship | 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. | en_US |
dc.language.iso | en_US | en_US |
dc.publisher | Springer | en_US |
dc.subject | RNA-seq | en_US |
dc.subject | Transcriptome | en_US |
dc.subject | Assembly | en_US |
dc.subject | Next-generation sequencing | en_US |
dc.subject | Quality control | en_US |
dc.subject | Expression analysis | en_US |
dc.title | RNA-seq for transcriptome analysis in non-model plants | en_US |
dc.title.alternative | Legume Genomics: methods and protocols | en_US |
dc.title.alternative | Springer Protocols | en_US |
dc.type | Book chapter | en_US |
Appears in Collections: | Institutional Publications |
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Jain M_2013_6.pdf Restricted Access | 252 kB | Adobe PDF | View/Open Request a copy |
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