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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RNA Sequencing Reveals Novel Gene Clusters in Bovine Conceptuses Associated with Maternal Recognition of Pregnancy and Implantation
Solomon Mamo,Jai Prakash Mehta,Paul A. McGettigan,Trudee Fair,Thomas E. Spencer,Fuller W. Bazer,Patrick Lonergan +6 more
TL;DR: This transcriptome analysis of the bovine conceptus will provide a blueprint of the dynamic changes in gene expression occurring during maternal recognition and implantation and will complement existing knowledge of the temporal changes in the endometrial transcriptome, thus facilitating a better understanding of conceptus-maternal cross talk during the peri-implantation period of pregnancy.
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Marine invasion genetics: from spatio-temporal patterns to evolutionary outcomes
TL;DR: There is a need for further investigations of evolutionary mechanisms that affect individual fitness and adaptation to rapid environmental change in marine biological invasions, as most studies reveal similar genetic diversity values in both native and introduced ranges.
Journal ArticleDOI
Direct RNA Sequencing of the Coding Complete Influenza A Virus Genome.
Matthew W. Keller,Benjamin L. Rambo-Martin,Malania M. Wilson,Callie A. Ridenour,Samuel S. Shepard,Thomas J. Stark,Elizabeth B Neuhaus,Vivien G. Dugan,David E. Wentworth,John R. Barnes +9 more
TL;DR: An adapter to short highly conserved termini of the influenza A virus genome is designed to target the (-) sense RNA into a protein nanopore on the Oxford Nanopore MinION sequencing platform, and successful sequencing is demonstrated.
Journal ArticleDOI
Serum, plasma and saliva biomarkers for head and neck cancer
Lidia Maria Rebolho Batista Arantes,Ana Carolina de Carvalho,Matias Eliseo Melendez,André Lopes Carvalho +3 more
TL;DR: This review will focus on the feasibility of evaluating molecular-based biomarkers in body fluids as markers for diagnosis, prognosis, and surveillance in head and neck squamous cell carcinoma patients.
Profiling the venom gland transcriptomes of costa rican snakes by 454 pyrosequencing
Jordi Durban,Paula Juárez,Yamileth Angulo,Bruno Lomonte,Marietta Flores-Díaz,Alberto Alape-Girón,Mahmood Sasa,José María Gutiérrez,Ana Conesa,Joaquín Dopazo,Juan J. Calvete +10 more
TL;DR: The comparative next-generation sequencing (NGS) analysis of snake venom transcriptomes reveals taxon-specific trends governing the formulation of the venom arsenal, and may represent the tool for opening the door to systems venomics.
References
More filters
Journal ArticleDOI
Mapping and quantifying mammalian transcriptomes by RNA-Seq.
TL;DR: Although >90% of uniquely mapped reads fell within known exons, the remaining data suggest new and revised gene models, including changed or additional promoters, exons and 3′ untranscribed regions, as well as new candidate microRNA precursors.
PatentDOI
Serial analysis of gene expression
Kenneth W. Kinzler,Victor Velculescu,Bert Vogelstein,Lin Zhang,ヴェルヴレスク，ヴィクター，イー．,ヴォゲルステイン，バート,キンズラー，ケネス，ダブリュ．,ツァン，リン +7 more
TL;DR: Serial analysis of gene expression (SAGE) should provide a broadly applicable means for the quantitative cataloging and comparison of expressed genes in a variety of normal, developmental, and disease states.
Journal ArticleDOI
Mapping short DNA sequencing reads and calling variants using mapping quality scores
Heng Li,Jue Ruan,Richard Durbin +2 more
TL;DR: This work describes the software MAQ, software that can build assemblies by mapping shotgun short reads to a reference genome, using quality scores to derive genotype calls of the consensus sequence of a diploid genome, e.g., from a human sample.
Journal ArticleDOI
RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
TL;DR: It is found that the Illumina sequencing data are highly replicable, with relatively little technical variation, and thus, for many purposes, it may suffice to sequence each mRNA sample only once (i.e., using one lane).
Journal ArticleDOI
SOAP: short oligonucleotide alignment program
TL;DR: The program SOAP is designed to handle the huge amounts of short reads generated by parallel sequencing using the new generation Illumina-Solexa sequencing technology, which supports multi-threaded parallel computing and has a batch module for multiple query sets.
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