RNA-Seq: a revolutionary tool for transcriptomics
Reads0
Chats0
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
More filters
Journal ArticleDOI
Overproduction of recombinant proteins in plants
TL;DR: The potential for plants to become one of the major avenues for protein production appears very promising, but it will take more time and effort to accomplish than has been the case for the simpler unicellular systems.
Journal ArticleDOI
Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future
Georgios A. Pavlopoulos,Dimitris Malliarakis,Nikolas Papanikolaou,Theodosis Theodosiou,Anton J. Enright,Ioannis Iliopoulos +5 more
TL;DR: The past, present and future of genomic and systems biology visualization is discussed, and the latest libraries and programming languages that enable more effective, efficient and faster approaches for visualizing biological concepts are focused on.
Journal ArticleDOI
Identifying (non-)coding RNAs and small peptides: Challenges and opportunities
TL;DR: Annotation studies in zebrafish are reviewed to discuss the challenges of placing RNAs onto the continuum that ranges from functional protein‐encoding mRNAs to potentially non‐functional peptide‐producing RNAs to non‐coding RNAs.
Journal ArticleDOI
Domestic dogs and cancer research: a breed-based genomics approach.
TL;DR: The meticulous record keeping associated with dog breeding makes the model still more powerful, as it facilitates both association analysis and family-based linkage studies, and the ability to diagnose and treat cancer in dogs and humans alike.
Journal ArticleDOI
NGS Technologies as a Turning Point in Rare Disease Research , Diagnosis and Treatment
TL;DR: The milestones achieved in the understanding of rare diseases since the emergence of next-generation sequencing (NGS) technologies are reviewed and how these advances have influenced research and diagnosis are analyzed.
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.
Related Papers (5)
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Full-length transcriptome assembly from RNA-Seq data without a reference genome.
Manfred Grabherr,Brian J. Haas,Moran Yassour,Moran Yassour,Joshua Z. Levin,Dawn Thompson,Ido Amit,Xian Adiconis,Lin Fan,Raktima Raychowdhury,Qiandong Zeng,Zehua Chen,Evan Mauceli,Nir Hacohen,Andreas Gnirke,Nicholas Rhind,Federica Di Palma,Bruce W. Birren,Chad Nusbaum,Kerstin Lindblad-Toh,Kerstin Lindblad-Toh,Nir Friedman,Aviv Regev +22 more