Abstract：
:RNA sequencing has become an important method to perform hypothesis-free characterization of global gene expression. One of the limitations of RNA sequencing is that most sequence reads represent highly expressed transcripts, whereas low level transcripts are challenging to detect. To combine the benefits of traditional expression arrays with the advantages of RNA sequencing, we have used whole exome enrichment prior to sequencing of total RNA. We show that whole exome capture can be successfully applied to cDNA to study the transcriptional landscape in human tissues. By introducing the exome enrichment step, we are able to identify transcripts present at very low levels, which are below the level of detection in conventional RNA sequencing. Although the enrichment increases the ability to detect presence of transcripts, it also lowers the accuracy of quantification of expression levels. Our results yield a large number of novel exons and splice isoforms, suggesting that conventional RNA sequencing methods only detect a small fraction of the full transcript diversity. We propose that whole exome enrichment of RNA is a suitable strategy for genome-wide discovery of novel transcripts, alternative splice variants and fusion genes.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Halvardson J,Zaghlool A,Feuk Ldoi
10.1093/nar/gks816subject
Has Abstractpub_date
2013-01-07 00:00:00pages
e6issue
1eissn
0305-1048issn
1362-4962pii
gks816journal_volume
41pub_type
杂志文章abstract：:The DNA sequence of a 225.4 kilobase segment of the Escherichia coli K-12 genome is described here, from 76.0 to 81.5 minutes on the genetic map. This brings the total of contiguous sequence from the E.coli genome project to 725.1 kb (76.0 to 92.8 minutes). We found 191 putative coding genes (ORFs) of which 72 genes w...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.13.2576
更新日期：1994-07-11 00:00:00
abstract：:The Comparative Toxicogenomics Database (CTD; http://ctdbase.org/) provides information about interactions between environmental chemicals and gene products and their relationships to diseases. Chemical-gene, chemical-disease and gene-disease interactions manually curated from the literature are integrated to generate...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks994
更新日期：2013-01-01 00:00:00
abstract：:Nuclear extracts prepared from growth hormone-secreting (GC) and prolactin-secreting (235-1) rat anterior pituitary cell lines were compared for their ability to bind to the DNA sequences conferring tissue-specificity to the expression of the rat growth hormone (rGH) gene promoter. Cell-specific differences in the int...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.17.5235
更新日期：1990-09-11 00:00:00
abstract：:The polyadenylate binding protein 1 (PABPN1) is a ubiquitously expressed RNA binding protein vital for multiple steps in RNA metabolism. Although PABPN1 plays a critical role in the regulation of RNA processing, mutation of the gene encoding this ubiquitously expressed RNA binding protein causes a specific form of mus...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx786
更新日期：2017-10-13 00:00:00
abstract：:Aberration within the p53 tumor suppressor gene is the most frequently identified genetic damage in human cancer. Regulatory functions proposed for the p53 protein include modulation of the cell cycle, cellular differentiation, signal transduction, and gene expression. Additionally, the p53 gene product may guard the ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.3.713
更新日期：1993-02-11 00:00:00
abstract：:The binding of two symmetric bis-benzimidazole compounds, 2,2-bis-[4'-(3"-dimethylamino-1"-propyloxy)phenyl]-5,5-bi-1H-benzimidazole and its piperidinpropylphenyl analog, to the minor groove of DNA, have been studied by DNA footprinting, surface plasmon resonance (SPR) methods and molecular dynamics simulations in exp...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg237
更新日期：2003-03-01 00:00:00
abstract：:We developed an integrated method to identify aptamers with only 10 fixed nucleotides through ligation and removal of primer binding sites within the systematic evolution of ligands by exponential enrichment (SELEX) process. This Tailored-SELEX approach was validated by identifying a Spiegelmer ('mirror-image aptamer'...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gng130
更新日期：2003-11-01 00:00:00
abstract：:The principal early promoter of human papillomaviruses (HPVs), designated P97 in the case of HPV-16, contains four characteristically aligned cis-responsive elements, namely one binding site for Sp1, two for the viral E2 proteins, and the TATA box. The Sp1 binding site is needed to mediate activation of P97 by the rem...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.2.251
更新日期：1992-01-25 00:00:00
abstract：:DNA transposon-based vectors have emerged as gene vehicles with a wide biomedical and therapeutic potential. So far, genomic insertion of such vectors has relied on the co-delivery of genetic material encoding the gene-inserting transposase protein, raising concerns related to persistent expression, insertional mutage...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt1163
更新日期：2014-02-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.suppl.r403
更新日期：1988-01-01 00:00:00
abstract：:RNA is ideally suited for in vitro evolution experiments, because a single RNA molecule possesses both genotypic (replicable sequence) and phenotypic (selectable shape) properties. Using systematic evolution of ligands by exponential enrichment (SELEX), we found a single 58-nt aptamer sequence that assumes two structu...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp284
更新日期：2009-07-01 00:00:00
abstract：:The J-binding protein 1 (JBP1) is essential for biosynthesis and maintenance of DNA base-J (β-d-glucosyl-hydroxymethyluracil). Base-J and JBP1 are confined to some pathogenic protozoa and are absent from higher eukaryotes, prokaryotes and viruses. We show that JBP1 recognizes J-containing DNA (J-DNA) through a 160-res...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr125
更新日期：2011-07-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm956
更新日期：2008-01-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.6.1463
更新日期：1981-03-25 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn098
更新日期：2008-05-01 00:00:00
abstract：:Using a genetic selection for suppressors of a UGA nonsense mutation in trpA, we have isolated a G to A transition mutation at position 1491 in the decoding region of 16S rRNA. This suppressor displayed no codon specificity, suppressing UGA, UAG and UAA nonsense mutations and +1 and -1 frameshift mutations in lacZ. Su...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.21.4234
更新日期：1995-11-11 00:00:00
abstract：:We present a www server for AUGUSTUS, a novel software program for ab initio gene prediction in eukaryotic genomic sequences. Our method is based on a generalized Hidden Markov Model with a new method for modeling the intron length distribution. This method allows approximation of the true intron length distribution m...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh379
更新日期：2004-07-01 00:00:00
abstract：:MCScan is an algorithm able to scan multiple genomes or subgenomes in order to identify putative homologous chromosomal regions, and align these regions using genes as anchors. The MCScanX toolkit implements an adjusted MCScan algorithm for detection of synteny and collinearity that extends the original software by in...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr1293
更新日期：2012-04-01 00:00:00
abstract：:Repression of cellular reprogramming in germ cells is critical to maintaining cell fate and fertility. When germ cells mis-express somatic genes they can be directly converted into other cell types, resulting in loss of totipotency and reproductive potential. Identifying the molecular mechanisms that coordinate these ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa174
更新日期：2020-05-07 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
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更新日期：2017-11-02 00:00:00
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journal_title：Nucleic acids research
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更新日期：1983-07-11 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gng045
更新日期：2003-04-15 00:00:00
abstract：:Conserved in a variety of evolutionarily divergent plant species, LOB DOMAIN (LBD) genes define a large, plant-specific family of largely unknown function. LBD genes have been implicated in a variety of developmental processes in plants, although to date, relatively few members have been assigned functions. LBD protei...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm775
更新日期：2007-01-01 00:00:00
abstract：:We describe a rapid fluorescence indicator displacement assay (R-FID) to evaluate the affinity and the selectivity of compounds binding to different DNA structures. We validated the assay using a library of 30 well-known nucleic acid binders containing a variety chemical scaffolds. We used a combination of principal c...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky019
更新日期：2018-04-20 00:00:00
abstract：:Single-stranded mRNA molecules form secondary structures through complementary self-interactions. Several hypotheses have been proposed on the relationship between the nucleotide sequence, encoded amino acid sequence and mRNA secondary structure. We performed the first transcriptome-wide in silico analysis of the huma...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl287
更新日期：2006-05-08 00:00:00
abstract：:The International Mouse Phenotyping Consortium (IMPC) web portal (http://www.mousephenotype.org) provides the biomedical community with a unified point of access to mutant mice and rich collection of related emerging and existing mouse phenotype data. IMPC mouse clinics worldwide follow rigorous highly structured and ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt977
更新日期：2014-01-01 00:00:00
abstract：:The excision of specific DNA sequences from integrated transgenes in insects permits the dissection in situ of structural elements that may be important in controlling gene expression. Furthermore, manipulation of potential control elements in the context of a single integration site mitigates against insertion site i...
journal_title：Nucleic acids research
pub_type： 杂志文章
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更新日期：2003-11-15 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm057
更新日期：2007-01-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt915
更新日期：2014-01-01 00:00:00
abstract：:Next-generation sequencing technologies have made it possible to carry out transcriptome analysis at the single-cell level. Single-cell RNA-sequencing (scRNA-seq) data provide insights into cellular dynamics, including intercellular heterogeneity as well as inter- and intra-cellular fluctuations in gene expression tha...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz181
更新日期：2019-05-21 00:00:00
