Abstract
RNA expression profiles produced by next-generation sequencing (NGS) technology (RNA-seq) allow comprehensive investigation of transcribed sequences within a cell or tissue. RNA-seq is rapidly becoming more cost-effective for transcriptome profiling. However, its usage will expand dramatically if one starts with low amount of RNA and obtains transcript directionality during the analysis. Here, we describe a detailed protocol for the creation of a directional RNA-seq library from 100 ng of starting total RNA.
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Web Resources/URLs
Ensembl: http://www.ensembl.org
UCSC Genome Browser: http://www.genome.ucsc.edu
Illumina, Inc: http://illumina.com
Burrows-Wheeler Aligner (BWA): http://bio-bwa.sourceforge.net/
TopHat: http://tophat.cbcb.umd.edu
Cufflinks: http://cufflinks.cbcb.umd.edu
NovoAlign: http://www.novocraft.com/main/index.php
CLC Bio Genomics Workbench: http://www.clcbio.com/
Partek: http://www.partek.com/
Strand Life Sciences Avadis NGS: http://www.strandls.com/
Acknowledgment
The authors are supported by Intramural Research Program of the National Eye Institute, National Institutes of Health, Bethesda, MD, USA.
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Brooks, M.J., Rajasimha, H.K., Swaroop, A. (2012). Retinal Transcriptome Profiling by Directional Next-Generation Sequencing Using 100 ng of Total RNA. In: Wang, SZ. (eds) Retinal Development. Methods in Molecular Biology, vol 884. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-848-1_23
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DOI: https://doi.org/10.1007/978-1-61779-848-1_23
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Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-61779-847-4
Online ISBN: 978-1-61779-848-1
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