The DOI matches its Crossref record; 20 of the 20 references it cites were found in a registry or an index.
RNA‐Seq: A Method for Comprehensive Transcriptome Analysis
Abstract
A recently developed technique called RNA Sequencing (RNA‐Seq) uses massively parallel sequencing to allow transcriptome analyses of genomes at a far higher resolution than is available with Sanger sequencing‐ and microarray‐based methods. In the RNA‐Seq method, complementary DNAs (cDNAs) generated from the RNA of interest are directly sequenced using next‐generation sequencing technologies. The reads obtained from this can then be aligned to a reference genome in order to construct a whole‐genome transcriptome map. RNA‐Seq has been used successfully to precisely quantify transcript levels, confirm or revise previously annotated 5′ and 3′ ends of genes, and map exon/intron boundaries. This unit describes protocols for performing RNA‐Seq using the Illumina sequencing platform. Curr. Protoc. Mol. Biol. 89:4.11.1‐4.11.13. © 2010 by John Wiley & Sons, Inc.
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Mapping and quantifying mammalian transcriptomes by RNA-Seq
Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., & Wold, B. (2008) · Nature Methods · doi:10.1038/nmeth.1226 · Cited by 13,696
RNA-Seq: a revolutionary tool for transcriptomics
Wang, Z., Gerstein, M., & Snyder, M. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2484 · Cited by 13,174
Self-citation<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool
Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480
SOAP: Short oligonucleotide alignment program
Li, R., Li, Y., Kristiansen, K., & Wang, J. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn025 · Cited by 3,597
RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
Marioni, J. C., Mason, C. E., Mane, S. M., Stephens, M., & Gilad, Y. (2008) · Genome Research · doi:10.1101/gr.079558.108 · Cited by 2,771
The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing
Nagalakshmi, U., Wang, Z., Waern, K., Shou, C., Raha, D., Gerstein, M., & Snyder, M. (2008) · Science · doi:10.1126/science.1158441 · Cited by 2,479
Self-citationHighly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis
Lister, R., O'Malley, R. C., Tonti-Filippini, J., Gregory, B. D., Berry, C. C., Millar, A. H., & Ecker, J. R. (2008) · Cell · doi:10.1016/j.cell.2008.03.029 · Cited by 2,418
The impact of next-generation sequencing technology on genetics
Mardis, E. R. (2008) · Trends in Genetics · doi:10.1016/j.tig.2007.12.007 · Cited by 2,053
Sultan, M., Schulz, M. H., Richard, H., Magen, A., Klingenhoff, A., Scherf, M., Seifert, M., Borodina, T., Soldatov, A., Parkhomchuk, D., et al. (2008) · Science · doi:10.1126/science.1160342 · Cited by 1,293
Applications of next-generation sequencing technologies in functional genomics
Morozova, O., & Marra, M. A. (2008) · Genomics · doi:10.1016/j.ygeno.2008.07.001 · Cited by 1,188
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Manzoni, C., Kia, D. A., Vandrovcova, J., Hardy, J., Wood, N. W., Lewis, P. A., & Ferrari, R. (2018) · Briefings in Bioinformatics · doi:10.1093/bib/bbw114 · Cited by 804
Microarrays, deep sequencing and the true measure of the transcriptome
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Metadata
- Authors
- Nagalakshmi, U., Waern, K., & Snyder, M.
- Venue
- Current Protocols in Molecular Biology
- Publisher
- Wiley
- Published
- 2010-01
- Volume
- 89
- Issue
- 1
- Pages
- Unit 4.11.1-13
- ISSN
- 1934-3639 (ISSN-L)
- 1934-3647
- OpenAlex
- W1843238398
- Cited by
- 324
- References
- 20
- FWCI
- 8.15
- Type
- journal article
- Language
- en
- Open access
- closed
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