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
CircNet: a database of circular RNAs derived from transcriptome sequencing data
Yu-Chen Liu,Jian-Rong Li,Chuan-Hu Sun,Erik Andrews,Rou-Fang Chao,Feng Mao Lin,Shun Long Weng,Shun Long Weng,Sheng Da Hsu,Chieh-Chen Huang,Chao Cheng,Chun-Chi Liu,Hsien Da Huang +12 more
TL;DR: The CircNet database is to the authors' knowledge the first public database that provides tissue-specific circRNA expression profiles and circRNA–miRNA-gene regulatory networks and generates an integrated regulatory network that illustrates the regulation between circRNAs, miRNAs and genes.
Journal ArticleDOI
Profiling gene expression responses of coral larvae (Acropora millepora) to elevated temperature and settlement inducers using a novel RNA-Seq procedure.
TL;DR: A novel RNA‐Seq protocol was applied to study molecular responses to heat and settlement inducers in aposymbiotic larvae of the reef‐building coral Acropora millepora to reveal extensive variation in these responses depending on genetic background, including qualitative differences.
Journal ArticleDOI
Use of Metatranscriptomics in Microbiome Research
TL;DR: Some of the key metatranscriptomics strategies that are implemented to determine microbiota gene expression and its regulation are highlighted and discussed and the advantages and potential challenges associated with these approaches are discussed.
Journal ArticleDOI
Altered distributions of Gemini of coiled bodies and mitochondria in motor neurons of TDP-43 transgenic mice
TL;DR: Findings indicate that TDP-43 participates in pathways critical for motor neuron physiology, including those that regulate the normal distributions of SMN-associated GEMs in the nucleus and mitochondria in the cytoplasm.
Journal ArticleDOI
CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains
Patrick R. Wright,Jens Georg,Martin Mann,Dragos Alexandru Sorescu,Andreas S. Richter,Steffen C. Lott,Robert Kleinkauf,Wolfgang R. Hess,Rolf Backofen +8 more
TL;DR: The functionality of the CopraRNA and IntaRNA webservers are introduced and detailed explanations on their postprocessing functionalities are given.
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