RNA-Seq: a revolutionary tool for transcriptomics
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119 citations
Cites methods from "RNA-Seq: a revolutionary tool for t..."
...RNA deep sequencing (RNA-seq) techniques such as Illumina and SOLiD sequencing are commonly used techniques for high-throughput transcriptome analysis (further details on these and other RNA sequencing techniques are reviewed in Wang et al., 2009)....
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118 citations
Cites background from "RNA-Seq: a revolutionary tool for t..."
...Importantly, the generation of large amounts of DNA sequence data from related species will allow comparative genomic approaches for the identification of trait loci, and this is particularly so with transcriptome sequencing (‘RNA-seq’; Wang et al. 2009)....
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118 citations
Cites background or methods from "RNA-Seq: a revolutionary tool for t..."
...The 454 direct sequencing approach is also characterized by a smaller intrinsic error rate than conventional Sanger-based sequencing technology.((66,67))...
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...With a single sequencing run, several hundred gene-specific PCR amplicons together with several hundred genomic control fragments can be analyzed obtaining coverage of about 1,000 reads per cDNA fragment.((66,67)) This would allow for the detection of editing events with a sub-percentage penetrance....
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...For example, the 454 KS GLS platform (Roche) with average read lengths of 250 bp is well suited for this purpose.((66,67)) With a single sequencing run, several hundred gene-specific PCR amplicons together with several hundred genomic control fragments can be analyzed obtaining coverage of about 1,000 reads per cDNA fragment....
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118 citations
Cites background from "RNA-Seq: a revolutionary tool for t..."
...The advent of RNA-Seq technology, in which the entire polyadenylated transcriptome is sequenced [19-24], is capable of building on this microarray data to provide additional insights into the transcriptome of the airway epithelium and its response to cigarette smoke....
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...The development of massive parallel RNA sequencing (RNA-Seq) technology permits quantitative assessment of poly(A) mRNA levels to a high degree of sensitivity [19-24]....
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...Because RNA-Seq provides direct sequencing information of all polyadenylated mRNAs and is not limited by probe design, RNA-Seq data has inherently less noise and higher specificity, and, importantly, provides quantitative information on mRNA transcript number [19]....
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118 citations
Cites methods from "RNA-Seq: a revolutionary tool for t..."
...Digital expression profiling (or RNA-seq) is a powerful and efficient approach for large-scale gene expression analysis [23]....
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References
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"RNA-Seq: a revolutionary tool for t..." refers methods in this paper
...There are several programs for mapping reads to the genome, including ELAND, SOA...
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