Mapping and quantifying mammalian transcriptomes by RNA-Seq

@article{Mortazavi2008MappingAQ,
  title={Mapping and quantifying mammalian transcriptomes by RNA-Seq},
  author={Ali Mortazavi and Brian A. Williams and Kenneth McCue and Lorian Schaeffer and Barbara J. Wold},
  journal={Nature Methods},
  year={2008},
  volume={5},
  pages={621-628}
}
We have mapped and quantified mouse transcriptomes by deeply sequencing them and recording how frequently each gene is represented in the sequence sample (RNA-Seq). This provides a digital measure of the presence and prevalence of transcripts from known and previously unknown genes. We report reference measurements composed of 41–52 million mapped 25-base-pair reads for poly(A)-selected RNA from adult mouse brain, liver and skeletal muscle tissues. We used RNA standards to quantify transcript… Expand
Spliced synthetic genes as internal controls in RNA sequencing experiments
TLDR
A set of spike-in RNA standards, termed 'sequins' (sequencing spike-ins), that represent full-length spliced mRNA isoforms, that provide a qualitative and quantitative reference with which to navigate the complexity of the human transcriptome are developed. Expand
Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms
High-throughput mRNA sequencing (RNA-Seq) promises simultaneous transcript discovery and abundance estimation. However, this would require algorithms that are not restricted by prior gene annotationsExpand
Errors in RNA-Seq quantification affect genes of relevance to human disease
TLDR
It is shown that it is possible to use data that may otherwise have been discarded to measure group-level expression, and that such data contains biologically relevant information. Expand
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation.
TLDR
The results suggest that Cufflinks can illuminate the substantial regulatory flexibility and complexity in even this well-studied model of muscle development and that it can improve transcriptome-based genome annotation. Expand
Transcriptomics: Digging deep with RNA-Seq
TLDR
Two new studies have surveyed the transcriptomes of model yeast species and identify large numbers of previously unknown transcripts, provide new information about the positions of promoters, exons and 3′ ends, and highlight the enormous level of transcript diversity that can be generated by alternative splicing in mammals. Expand
Advancing RNA-Seq analysis
TLDR
New approaches for RNA-Seq analysis that capture genome-wide transcription and splicing in unprecedented detail are introduced, and a de novo assembly approach implemented in the ABySS software reduces the annotation problem to that of aligning full-length cDNAs, which is well handled by several algorithms. Expand
Accurate quantification of transcriptome from RNA-Seq data by effective length normalization
TLDR
It is proposed that NEUMA could make a standard method in quantifying gene transcript levels from RNA-Seq data and offers a measure of consistency (‘consistency coefficient’) for each gene between an independently measured gene-wise level and the sum of the isoform levels. Expand
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
TLDR
It is shown that accurate gene-level abundance estimates are best obtained with large numbers of short single-end reads, and estimates of the relative frequencies of isoforms within single genes may be improved through the use of paired- end reads, depending on the number of possible splice forms for each gene. Expand
RNA-Sequencing and Methylome Analysis
TLDR
This chapter discusses the concepts and considerations of RNA-seq and methylome sequencing, and describes the basic approaches and challenges associated with these applications. Expand
A single-molecule long-read survey of the human transcriptome
TLDR
The results show the feasibility of deep sequencing full-length RNA from complex eukaryotic transcriptomes on a single-molecule level and high-confidence mappings are consistent with GENCODE annotations. Expand
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 24 REFERENCES
Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution
TLDR
High-throughput sequencing of complementary DNAs (RNA-Seq) and strand-specific array data provide rich condition-specific information on novel, mostly non-coding transcripts, untranslated regions and gene structures, thus improving the existing genome annotation. Expand
The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing
TLDR
A quantitative sequencing-based method is developed for mapping transcribed regions, in which complementary DNA fragments are subjected to high-throughput sequencing and mapped to the genome, and it is demonstrated that most (74.5%) of the nonrepetitive sequence of the yeast genome is transcribed. Expand
Tag-based approaches for transcriptome research and genome annotation
TLDR
The 5′ end–specific tags, with their ability to identify transcripts along with their transcriptional start sites, will be of particular interest for gene network studies and may become one of the most important approaches in systems biology. Expand
Shotgun sequencing of the human transcriptome with ORF expressed sequence tags.
TLDR
Theoretical considerations predict that amplification of expressed gene transcripts by reverse transcription-PCR using arbitrarily chosen primers will result in the preferential amplification of the central portion of the transcript, and this approach should make a significant contribution to the early identification of important human genes. Expand
Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis
TLDR
Deep sequencing of smRNAs revealed a direct relationship between the location of sm RNAs and DNA methylation, perturbation of smRNA biogenesis upon loss of CpG DNA methylisation, and a tendency for smRN as to direct strand-specific DNA methylations in regions of RNA-DNA homology. Expand
Genome-Wide Survey of Human Alternative Pre-mRNA Splicing with Exon Junction Microarrays
TLDR
These genome-wide data provide experimental evidence and tissue distributions for thousands of known and novel alternative splicing events and indicate that at least 74% of human multi-exon genes are alternatively spliced. Expand
Global Identification of Human Transcribed Sequences with Genome Tiling Arrays
TLDR
This work constructed a series of high-density oligonucleotide tiling arrays representing sense and antisense strands of the entire nonrepetitive sequence of the human genome and found 10,595 transcribed sequences not detected by other methods. Expand
RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription
TLDR
Three potentially functional classes of RNAs have been identified, two of which are syntenically conserved and correlate with the expression state of protein-coding genes and support a highly interleaved organization of the human transcriptome. Expand
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).
TLDR
Comparison of the sequence of the MGC clones to reference genome sequences reveals that most cDNA clones are of very high sequence quality, although it is likely that some cDNAs may carry missense variants as a consequence of experimental artifact, such as PCR, cloning, or reverse transcriptase errors. Expand
Transcriptional Maps of 10 Human Chromosomes at 5-Nucleotide Resolution
TLDR
The transcribed portions of the human genome are predominantly composed of interlaced networks of both poly A+ and poly A– annotated transcripts and unannotated transcripts of unknown function, which has important implications for interpreting genotype-phenotype associations, regulation of gene expression, and the definition of a gene. Expand
...
1
2
3
...