RNA-Seq: a revolutionary tool for transcriptomics
TLDR
The RNA-Seq approach to transcriptome profiling that uses deep-sequencing technologies provides a far more precise measurement of levels of transcripts and their isoforms than other methods.Abstract:
RNA-Seq is a recently developed approach to transcriptome profiling that uses deep-sequencing technologies. Studies using this method have already altered our view of the extent and complexity of eukaryotic transcriptomes. RNA-Seq also provides a far more precise measurement of levels of transcripts and their isoforms than other methods. This article describes the RNA-Seq approach, the challenges associated with its application, and the advances made so far in characterizing several eukaryote transcriptomes.read more
Citations
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Journal ArticleDOI
Cis and Trans Acting Factors Involved in Human Cytomegalovirus Experimental and Natural Latent Infection of CD14 (+) Monocytes and CD34 (+) Cells
TL;DR: Next generation sequencing deduced the transcriptome of HCMV latently infected CD14 (+) and CD34 (+) cells in experimental as well as natural latency settings and showed that the terminal repeat (TR) region of the latent viral genome is depleted of nucleosomes suggesting that this region may contain an element mediating viral genome maintenance.
Journal ArticleDOI
A model based criterion for gene expression calls using RNA-seq data.
TL;DR: A statistical model is suggested that considers the number of transcripts detected in a RNA-seq study as a mixture of two distributions: one is a exponential distribution for transcripts from inactive genes, and a negative binomial distribution for actively transcribed genes.
Journal ArticleDOI
FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data
Andrea Sboner,Lukas Habegger,Dorothee Pflueger,Stéphane Terry,David Z. Chen,Joel Rozowsky,Ashutosh K. Tewari,Naoki Kitabayashi,Benjamin J. Moss,Mark S. Chee,Francesca Demichelis,Mark A. Rubin,Mark Gerstein +12 more
TL;DR: FusionSeq detected known and novel fusions in a specially sequenced calibration data set, including eight cancers with and without known rearrangements, and ranks candidates according to several statistics.
Journal ArticleDOI
A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling
TL;DR: This study demonstrates that data from a SOLiD RNA-Seq experiment are sufficient to generate results comparable to those produced from Affymetrix Exon arrays, even using only a single replicate from each platform, and when presented with a large genome.
Journal ArticleDOI
Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples
Serban Nacu,Wenlin Yuan,Zhengyan Kan,Deepali Bhatt,Celina Sanchez Rivers,Jeremy Stinson,Brock A. Peters,Zora Modrusan,Kenneth Jung,Somasekar Seshagiri,Thomas D. Wu +10 more
TL;DR: Deep transcriptional sequencing and analysis with targeted and spliced alignment methods can effectively identify TIC events across the genome in individual tissues, involving more genes than estimated previously using ESTs.
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